Researcher Profile and Settings

Master

Affiliation (Master)

• Research Faculty of Agriculture　Fundamental AgriScience Research　Animal Science

Affiliation (Master)

• Research Faculty of Agriculture　Fundamental AgriScience Research　Animal Science

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Profile and Settings

Profile and Settings

• Name (Japanese)

  Koike

• Name (Kana)

  Satoshi

• Name

  200901072163996331

Achievement

Research Interests

• 消化管微生物   家畜栄養学   分子生態学   植物繊維分解   ルーメン   反芻動物   molecular ecology   Plant fiber degradation   Rumen microbes   

Research Areas

• Life sciences / Animal production science

Research Experience

• 2022/04 - Today Hokkaido University Research Faculty of Agriculture Professor
• 2015/10 - 2022/03 Hokkaido University Research Faculty of Agriculture Associate Professor
• 2007/04 - 2015/09 Hokkaido University Research Faculty of Agriculture Assistant Professor
• 2006/01 - 2007/03 Hokkaido University Creative Research Institute Sosei Assistant Professor
• 2003/02 - 2005/12 University of Illinois at Urbana-Champaign Postdoctoral fellow

Education

•        - 2003  Hokkaido University
•        - 2003  Hokkaido University  Graduate School, Division of Agriculture
•        - 2000  Mie University
•        - 2000  Mie University  Graduate School, Division of Bioresources
•        - 1998  Mie University  Faculty of Bioresources
•        - 1998  Mie University  Faculty of Bioresources

Committee Memberships

• 2021/04 - Today   Animal Science Journal   Associate Editor

Awards

• 2019/03 日本畜産学会 Animal Science Journalレビュアー賞
  
• 2017/01 AJAS 2016 Best Reviewer Award
   

  受賞者: KOIKE Satoshi
• 2015/03 日本畜産学会 Animal Science Journal Reviewers Award
  
• 2011 Animal Science Journal Excellent Paper Award
  
• 2007 日本畜産学会奨励賞
  

Published Papers

• Isolation and characterization of tannin‐degrading bacteria from the rumen of wild Hokkaido sika deer (Cervus nippon yezoensis)

  Yoshihiko Sawabe, Hidehisa Yamano, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 2024/01
• In vitro Effects of Cellulose Acetate on Fermentation Profiles, the Microbiome, and Gamma-aminobutyric Acid Production in Human Stool Cultures

  Hiroaki Yamada, Hiroto Miura, Yutaka Suzuki, Satoshi Koike, Shu Shimamoto, Yasuo Kobayashi

  Current Microbiology 80 (9) 0343-8651 2023/07/14
• Aristaeella hokkaidonensis gen. nov. sp. nov. and Aristaeella lactis sp. nov., two rumen bacterial species of a novel proposed family, Aristaeellaceae fam. nov.

  Sam C. Mahoney-Kurpe, Nikola Palevich, Samantha J. Noel, Dragana Gagic, Patrick J. Biggs, Priya Soni, Peter M. Reid, Satoshi Koike, Yasuo Kobayashi, Peter H. Janssen, Graeme T. Attwood, Christina D. Moon

  International Journal of Systematic and Evolutionary Microbiology 2023/05/12
• Batch culture analysis to identify potent organic acids for suppressing ruminal methane production

  Kyouko Yamada, Keiichiro Iwamae, Yutaka Suzuki, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 2023/01
• Alterations in rumen microbiota via oral fiber administration during early life in dairy cows

  Heshan Kodithuwakku, Daiki Maruyama, Hisashi Owada, Yuto Watabe, Hiroto Miura, Yutaka Suzuki, Kazuo Hirano, Yasuo Kobayashi, Satoshi Koike

  Scientific Reports 12 (1) 2022/06 [Refereed][Not invited]
   

  Abstract Bacterial colonization in the rumen of pre-weaned ruminants is important for their growth and post-weaning productivity. This study evaluated the effects of oral fiber administration during the pre-weaning period on the development of rumen microbiota from pre-weaning to the first lactation period. Twenty female calves were assigned to control and treatment groups (n = 10 each). Animals in both groups were reared using a standard feeding program throughout the experiment, except for oral fiber administration (50–100 g/day/animal) from 3 days of age until weaning for the treatment group. Rumen content was collected during the pre-weaning period, growing period, and after parturition. Amplicon sequencing of the 16S rRNA gene revealed that oral fiber administration facilitated the early establishment of mature rumen microbiota, including a relatively higher abundance of Prevotella, Shuttleworthia, Mitsuokella, and Selenomonas. The difference in the rumen microbial composition between the dietary groups was observed even 21 days after parturition, with a significantly higher average milk yield in the first 30 days of lactation. Therefore, oral fiber administration to calves during the pre-weaning period altered rumen microbiota, and its effect might be long-lasting until the first parturition.
• Application of MinION Amplicon Sequencing to Buccal Swab Samples for Improving Resolution and Throughput of Rumen Microbiota Analysis

  Hiroto Miura, Masayuki Takeda, Megumi Yamaguchi, Yoshihisa Ohtani, Go Endo, Yasuhisa Masuda, Kaede Ito, Yoshio Nagura, Kunihiro Iwashita, Tomohiro Mitani, Yutaka Suzuki, Yasuo Kobayashi, Satoshi Koike

  Frontiers in Microbiology 13 783058 - 783058 2022/03/24 [Refereed][Not invited]
   

  The Illumina MiSeq platform has been widely used as a standard method for studying the rumen microbiota. However, the low resolution of taxonomic identification is the only disadvantage of MiSeq amplicon sequencing, as it targets a part of the 16S rRNA gene. In the present study, we performed three experiments to establish a high-resolution and high-throughput rumen microbial profiling approach using a combination of MinION platform and buccal swab sample, which is a proxy for rumen contents. In experiment 1, rumen contents and buccal swab samples were collected simultaneously from cannulated cattle (n = 6) and used for microbiota analysis using three different analytical workflows: amplicon sequencing of the V3–V4 region of the 16S rRNA gene using MiSeq and amplicon sequencing of near full-length 16S rRNA gene using MinION or PacBio Sequel II. All reads derived from the MinION and PacBio platforms were classified at the species-level. In experiment 2, rumen fluid samples were collected from beef cattle (n = 28) and used for 16S rRNA gene amplicon sequencing using the MinION platform to evaluate this sequencing platform for rumen microbiota analysis. We confirmed that the MinION platform allowed species-level taxa assignment for the predominant bacterial groups, which were previously identified at the family- and genus-level using the MiSeq platform. In experiment 3, buccal swab samples were collected from beef cattle (n = 30) and used for 16S rRNA gene amplicon sequencing using the MinION platform to validate the applicability of a combination of the MinION platform and buccal swab samples for rumen microbiota analysis. The distribution of predominant bacterial taxa in the buccal swab samples was similar to that in the rumen samples observed in experiment 2. Based on these results, we concluded that the combination of the MinION platform and buccal swab samples may be potentially applied for rumen microbial analysis in large-scale studies.
• Expression of chemerin in intestinal mucosa of calves with comparable expression level with other antimicrobial proteins

  Yutaka Suzuki, Kanako Kubota, Satoshi Haga, Hideaki Hayashi, Mutsumi Oishi, Hiroto Miura, Sanggun Roh, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 93 (1) 1344-3941 2022/01
• Rumen microbiota and its relation to fermentation in lactose-fed calves

  S. Koike, M. Ueno, H. Miura, A. Saegusa, K. Inouchi, Y. Inabu, T. Sugino, L.L. Guan, M. Oba, Y. Kobayashi

  Journal of Dairy Science 104 (10) 10744 - 10752 0022-0302 2021/10 [Refereed][Not invited]
   

  In our previous studies, we revealed the effect of lactose inclusion in calf starters on the growth performance and gut development of calves. We conducted the present study as a follow-up study to identify the shift in rumen microbiota and its relation to rumen fermentation when calves are fed a lactose-containing starter. Thirty Holstein bull calves were divided into 2 calf starter treatment groups: texturized calf starter (i.e., control; n = 15) or calf starter in which starch was replaced with lactose at 10% (i.e., LAC10; n = 15) on a dry matter basis. All calves were fed their respective treatment calf starter ad libitum from d 7, and kleingrass hay from d 35. Rumen digesta were collected on d 80 (i.e., 3 wk after weaning) and used to analyze rumen microbiota and fermentation products. There was no apparent effect of lactose feeding on the α-diversity and overall composition of rumen microbiota. Amplicon sequencing and real-time PCR quantification of the 16S rRNA gene confirmed that the abundance of butyrate-producing bacteria (i.e., Butyrivibrio group and Megasphaera elsdenii) did not differ between the control and LAC10 groups. Conversely, the relative abundance of Mitsuokella spp., which produce lactate, succinate, and acetate, was significantly higher in the rumen of calves that were fed lactose, whereas the lactate concentration did not differ between the control and LAC10 groups. These findings suggest that the lactate production can be elevated by an increase of Mitsuokella spp. and then converted into butyrate, not propionate, since the proportion of propionate was lower in lactose-fed calves. In addition, we observed a higher abundance of Coriobacteriaceae and Pseudoramibacter-Eubacterium in the LAC10 group. Both these bacterial taxa include acetate-producing bacteria, and a positive correlation between the acetate-to-propionate ratio and the abundance of Pseudoramibacter-Eubacterium was observed. Therefore, the higher abundance of Coriobacteriaceae, Mitsuokella spp., and Pseudoramibacter-Eubacterium in the rumen of lactose-fed calves partially explains the increase in the proportion of rumen acetate that was observed in our previous study.
• Effects of oral administration of timothy hay and psyllium on the growth performance and fecal microbiota of preweaning calves

  K.A.H.T. Kodithuwakku, H. Owada, H. Miura, D. Maruyama, K. Hirano, Y. Suzuki, Y. Kobayashi, S. Koike

  Journal of Dairy Science in press 0022-0302 2021/09 [Refereed][Not invited]
  
• Cashew nut shell liquid potentially mitigates methane emission from the feces of Thai native ruminant livestock by modifying fecal microbiota

  Chiaki Narabe, Saki Kamiyama, Mizuki Saito, Phoompong Boonsaen, Anchalee Khongpradit, Suriya Sawanon, Yutaka Suzuki, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 92 (1) e13614  1344-3941 2021/08/18 [Refereed][Not invited]
   

  The methane-mitigating potency of cashew nutshell liquid (CNSL) was evaluated by investigating gas production from batch cultures using feces from Thai native ruminants that had been incubated for different periods. Feces was obtained from four Thai native cattle and four swamp buffaloes reared under practical feeding conditions at the Kasetsart University farm, Thailand. Fecal slurry from the same farm was also included in the analysis. CNSL addition successfully suppressed the methane production potential of feces from both ruminants by shifting short chain fatty acid profiles towards propionate production. Methane mitigation continued for almost 150 days, although the degree of mitigation was more apparent from Day 0 to Day 30. Bacterial and archaeal community shifts with CNSL addition were observed in feces from both ruminants; specifically, Bacteroides increased, whereas Lachnospiraceae and Ruminococcaceae decreased in feces to which CNSL was added. Fecal slurry did not show marked changes in gas production with CNSL addition. The findings showed that the addition of CNSL to the feces of ruminants native to the Southeast Asian region can suppress methane emission. Because CNSL can be easily obtained as a byproduct of the local cashew industry in this region, its on-site application might be ideal.
• Addition of ginkgo fruit to cattle feces and slurry suppresses methane production by altering the microbial community structure

  Risa Shintani, Seongjin Oh, Yutaka Suzuki, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 92 (1) e13620  1344-3941 2021/08/17 [Refereed][Not invited]
   

  The effect of ginkgo fruit addition on methane production potential of cattle feces and slurry was assessed in relation to other fermentation products and the microbial community. Holstein cattle fresh feces and slurry were left at 30°C for 0, 30, 60, 90, and 180 days with/without ginkgo fruit to monitor the effect on fermentation potential. With the addition of ginkgo fruit, methane production potential of feces was reduced on Day 30 and thereafter, and that of slurry was consistently reduced over the experimental period. As a general trend, ginkgo fruit addition resulted in decreased acetate and increased propionate in feces and acetate accumulation in slurry. With ginkgo fruit addition, MiSeq analyses indicated decreases in methanogen (in particular Methanocorpusculum), Ruminococcaceae, and Clostridiaceae populations and increases in Bacteroidaceae and Porphyromonadaceae populations, which essentially agreed with quantitative real-time polymerase chain reaction (qPCR) assay results. These data indicate that direct addition of ginkgo fruit to cattle excreta is useful for reducing methane emissions by altering the microbial community structure. The application of ginkgo fruit to lower methane emissions from cattle excreta is, therefore, useful in cases in which the excreta is left without special management for a long period of time.
• Growth and morphologic response of rumen methanogenic archaea and bacteria to cashew nut shell liquid and its alkylphenol components

  Makimi Wakai, Shusuke Hayashi, Yuko Chiba, Satoshi Koike, Kyo Nagashima, Yasuo Kobayashi

  Animal Science Journal 92 (1) e13598  1344-3941 2021/08/05 [Refereed][Not invited]
   

  The growth and morphology of rumen methanogenic archaea (15 strains of 10 species in 5 genera, including 7 strains newly isolated in the present study) and bacteria (14 species in 12 genera) were investigated using unsupplemented in vitro pure cultures and cultures supplemented with cashew nut shell liquid (CNSL) and its phenolic compound components, anti-methanogenic agents for ruminant animals. Growth of most of the methanogens tested was inhibited by CNSL and alkylphenols at different concentrations ranging from 1.56 to 12.5 μg/ml. Of the alkylphenols tested, anacardic acid exhibited the most potent growth inhibition. Three gram-negative bacterial species involved in propionate production were resistant to CNSL and alkylphenols (>50 μg/ml). All the methanogens and bacteria that were sensitive to CNSL and alkylphenols exhibited altered morphology; disruption of the cell surface was notable, possibly due to surfactant activity of the tested materials. Cells division was inhibited in some organisms, with cell elongation and unclear septum formation observed. These results indicate that CNSL and alkylphenols, particularly anacardic acid, inhibit both rumen bacteria and methanogens in a selective manner, which could help mitigate rumen methane generation.
• Identification of the core rumen bacterial taxa and their population dynamics during the fattening period in Japanese Black cattle

  Hiroto Miura, Takuya Hashimoto, Yukiko Kawanishi, Hiroki Kawauchi, Ryo Inoue, Noriaki Shoji, Kunihiko Saito, Mario Sekiya, Yosuke Saito, Jumpei Yasuda, Chiemi Yonezawa, Tetsushiro Endo, Hirotaka Kasuya, Yutaka Suzuki, Yasuo Kobayashi, Satoshi Koike

  Animal Science Journal 92 (1) e13601  1344-3941 2021/07/27 [Refereed][Not invited]
   

  The rumen microbiota comprises a vast range of bacterial taxa, which may affect the production of high-quality meat in Japanese Black cattle. The aim of this study was to identify core rumen microbiota in rumen fluid samples collected from 74 Japanese Black cattle raised under different dietary conditions using 16S rRNA gene amplicon sequencing. In the rumen of fattening Japanese Black cattle, 10 bacterial taxa, showing >1% average relative abundance and >95% prevalence, irrespective of the dietary conditions and the fattening periods, were identified as the core rumen bacterial taxa, which accounted for approximately 80% of the rumen microbiota in Japanese Black cattle. Additionally, population dynamics of the core rumen bacterial taxa revealed two distinct patterns: Prevotella spp. and unclassified Bacteroidales decreased in the mid-fattening period, whereas unclassified Clostridiales, unclassified Ruminococcaceae, Ruminococcus spp., and unclassified Christensenellaceae increased during the same period. Therefore, the present study reports the wide distribution of the core rumen bacterial taxa in Japanese Black cattle, and the complementary nature of the population dynamics of these core taxa, which may ensure stable rumen fermentation during the fattening period.
• Effect of Bacillus subtilis C‐3102 supplementation in milk replacer on growth and rumen microbiota in preweaned calves

  Satoshi Koike, Machiho Ueno, Nobuhisa Ashida, Tomokazu Imabayashi, Yasuo Kobayashi

  Animal Science Journal 92 (1) e13580  1344-3941 2021/07/26 [Refereed][Not invited]
   

  We aimed to assess the effect of feeding Bacillus subtilis C-3102 on the growth and rumen microbiota in the preweaned calves. Twelve newborn Japanese Black calves were randomly allocated to either the control (n = 6) or the treatment (n = 6) groups in the present study. Calves in the treatment group were offered B. subtilis C-3102 supplemented milk replacer throughout the preweaning period. Rumen fermentation during the first 21 days of life seemed to be slightly suppressed by feeding B. subtilis C-3102. This fermentation shift was probably attributed to the lower abundance of the core members of rumen microbiota until 21 days of age in the calves fed B. subtilis C-3102. However, feeding B. subtilis C-3102 did not influence the abundance of the core members of rumen microbiota at 90 days of age. Distribution of Sharpea spp. and Megasphaera spp., which potentially contribute to low methane production and are regarded as beneficial rumen bacteria, was higher in the rumen of calves fed B. subtilis C-3102 at 90 days of age. These results suggest that B. subtilis C-3102 supplementation in milk replacer could potentially contribute to the improvement of feed efficiency after weaning via the establishment of beneficial rumen bacteria.
• Feeding cashew nut shell liquid decreases methane production from feces by altering fecal bacterial and archaeal communities in Thai local ruminants

  Koya Tamori, Bungo Matsunaga, Phoompong Boonsaen, Anchalee Khongpradit, Suriya Sawanon, Kyo Nagashima, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 92 (1) e13569  2021/05/30 [Refereed][Not invited]
   

  The effect of feeding cashew nut shell liquid (CNSL) on fecal fermentation products and microbiota was investigated in Thai native cattle and swamp buffaloes. Four of each animal were fed rice straw and concentrate diet with control pellets without CNSL for 4 weeks, followed by the same diet with pellets containing CNSL for another 4 weeks, so that CNSL was administered at a level of 4 g/100 kg body weight. Feces were collected the last 2 days in each feeding period. CNSL alkyl phenols were recovered from feces (16%-28%) in a similar proportion to those in the diet, indicating that most functional anacardic acid was not selectively removed throughout the digestive tract. In vitro production of gas from feces, particularly methane, decreased with CNSL feeding. The proportion of acetate in feces decreased with CNSL feeding, whereas that of propionate increased, without affecting total short-chain fatty acid concentration. CNSL feeding changed fecal microbial community, particularly in swamp buffaloes, which exhibited decreases in the frequencies of Treponema, unclassified Ruminococcaceae, and Methanomassiliicoccaceae. These results suggest that CNSL feeding alters not only rumen fermentation but also hindgut fermentation via modulation of the microbial community, thereby potentially attenuating methane emission from the feces of ruminant animals.
• Chemical and microbial characterization for fermentation of water-soluble cellulose acetate in human stool cultures

  Hiroaki Yamada, Yuto Watabe, Yutaka Suzuki, Satoshi Koike, Shu Shimamoto, Yasuo Kobayashi

  Journal of the Science of Food and Agriculture 101 (7) 2950 - 2960 0022-5142 2021/05 [Refereed][Not invited]
   

  BACKGROUND Water-soluble cellulose acetate (WSCA), a synthetic fiber source, was applied to human stool cultures and to pure cultures of representative Bacteroides species to characterize the fermentation properties of WSCA in the human gut, and to assess the potential availability of WSCA as a food or additive candidate.RESULTS All nine of the different types of WSCA tested here provided increased acetate levels in human stool cultures. Greater levels of deacetylation were observed as the degree of substitution of hydroxyl groups by acetyl groups decreased. Among the nine tested types of WSCA, CA-0.78-128 caused the largest shifts of the microbial community, including an increased abundance of members of the genus Bacteroides, especially Bacteroides uniformis. Of four representative human gut Bacteroides species, only B. uniformis grew in pure culture on WSCA to produce acetate actively.CONCLUSION Water-soluble cellulose acetate has the potential for dietary application in human and other monogastric animals, based on the enhanced production of short-chain fatty acids (SCFAs), in particular acetate, in the hindgut. Short-chain fatty acid production is caused by selective proliferation of specific gut bacteria belonging to the genus Bacteroides. (c) 2020 Society of Chemical Industry
• Effect of trehalose supplementation in milk replacer on the incidence of diarrhea and fecal microbiota in preweaned calves.

  Hiroto Miura, Kazuhisa Mukai, Keigo Sudo, Satoshi Haga, Yutaka Suzuki, Yasuo Kobayashi, Satoshi Koike

  Journal of Animal Science 99 (1) 1 - 9 2021/01/16 [Refereed][Not invited]
   

  Trehalose, a nonreducing disaccharide consisting of d-glucose with α,α-1,1 linkage, was evaluated as a functional material to improve the gut environment in preweaned calves. In experiment 1, 173 calves were divided into two groups; the trehalose group was fed trehalose at 30 g/animal/d with milk replacer during the suckling period, and the control group was fed nonsupplemented milk replacer. Medication frequency was lower in the trehalose group (P < 0.05). In experiment 2, calves (n = 20) were divided into two groups (control group [n = 10] and trehalose group [n = 10]) based on their body weight and reared under the same feeding regimens as in experiment 1. Fresh feces were collected from individual animals at the beginning of the trial (average age 11 d), 3 wk after trehalose feeding (experimental day 22), and 1 d before weaning, and the fecal score was recorded daily. Fecal samples were analyzed for fermentation parameters and microbiota. The fecal score was significantly lower in the trehalose group than in the control group in the early stage (at an age of 14 to 18 d; P < 0.05) of the suckling period. Calves fed trehalose tended to have a higher proportion of fecal butyrate on day 22 than calves in the control group (P = 0.08). Population sizes of Clostridium spp. were significantly lower (P = 0.036), whereas those of Dialister spp. and Eubacterium spp. tended to be higher in the feces of calves in the trehalose group on day 22 (P = 0.060 and P = 0.083). These observations indicate that trehalose feeding modulated the gut environment and partially contributed to the reduction in medication frequency observed in experiment 1.
• Microbial community structure of the bovine rumen as affected by feeding cashew nut shell liquid, a methane-inhibiting and propionate-enhancing agent.

  Chisato Su, Takumi Shinkai, Nodoka Miyazawa, Makoto Mitsumori, Osamu Enishi, Kyo Nagashima, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 92 (1) e13503  2021/01/04 [Refereed][Not invited]
   

  The effect of cashew nut shell liquid (CNSL) feeding on bacterial and archaeal community of the bovine rumen was investigated by analyzing clone libraries targeting 16S rRNA genes, methyl-coenzyme reductase A-encoding genes (mcrA), and their respective transcripts. Rumen samples were collected from three non-lactating cows fed on a hay and concentrate diet with or without CNSL supplementation. DNA and complementary DNA (cDNA) libraries were generated for investigating rumen microbial communities. MiSeq analysis also was performed to understand more comprehensively the changes in the microbial community structures. Following CNSL supplementation, the number of operational taxonomical unit (OTU) and diversity indices of bacterial and archaeal community were decreased. Bacterial OTUs belonging to Proteobacteria, including Succinivibrio, occurred at a higher frequency with CNSL feeding, especially in cDNA libraries. The methanogenic archaeal community became dominated by Methanomicrobium. A bacterial community shift also was observed in the MiSeq data, indicating that CNSL increased the proportion of Succinivibrio and other genera known to be involved in propionate production. Methanogenic archaeal community shifts to increase Methanoplanus and to decrease Methanobrevibacter also were observed. Together, these results imply the occurrence of significant changes in rumen communities, not only for bacteria but also for methanogens, following CNSL feeding.
• The bio-surfactant mannosylerythritol lipid acts as a selective antibacterial agent to modulate rumen fermentation.

  Kana Okuhira, Satoshi Koike, Shinji Ito, Yasuo Kobayashi

  Animal Science Journal 91 (1) e13464  2020/10/05 [Refereed][Not invited]
   

  Methyl-mannosylerythritol lipid (MEL), a new sugar esterified lipid synthesized by Pseudozyma aphidis, was assessed for its functionality in modulating rumen fermentation and microbiota toward more propionate and less methane production. A pure culture study using rumen representatives showed that MEL selectively inhibited the growth of most Gram-positive bacteria including Streptococcus bovis, ruminococci, and Fibrobacter succinogenes, but not Gram-negative bacteria such as Megasphaera elsdenii, Succinivibrio dextrinosolvens, and Selenomonas ruminantium. A batch culture study revealed that MEL significantly decreased methane production in a dose-dependent manner with accumulation of hydrogen, while propionate production was enhanced. A continuous culture (Rusitec) study confirmed all of these changes. A feeding study revealed that sheep fed a MEL diet showed an increased proportion of propionate, while proportions of acetate and butyrate were decreased without affecting total VFA level. These changes disappeared after cessation of MEL feeding. Based on these results, dietary application of MEL can favorably modify rumen fermentation in terms of the efficiency of dietary energy utilization.
• Effect of pineapple stem starch feeding on rumen microbial fermentation, blood lipid profile, and growth performance of fattening cattle.

  Anchalee Khongpradit, Phoompong Boonsaen, Nitipong Homwong, Yutaka Suzuki, Satoshi Koike, Suriya Sawanon, Yasuo Kobayashi

  Animal Science Journal 91 (1) e13459  2020/09/29 [Refereed][Not invited]
   

  Pineapple stem starch (PS) was evaluated for its suitability as a new starch source in concentrate for fattening cattle, based on the growth performance, blood profile, and rumen parameters of 36 steers in a 206-day feeding study. PS was formulated as a 40% concentrate and fed with forage in comparison with ground corn (GC) and ground cassava (CA) formulated at the same level. PS feeding improved weight gain and feed conversion ratio without affecting feed intake. PS did not obviously influence blood lipid profiles throughout the experiment. Ruminal concentration of total short-chain fatty acids (SCFA) increased with PS without affecting SCFA composition throughout the feeding study. Rumen amylolytic group, especially Ruminococcus bromii, was dominant in the rumen microbial community, and showed increased abundance by PS feeding throughout the experiment. These results clearly indicate the potential of PS as a useful starch source for fattening cattle in terms of rumen fermentation and growth performance.
• Comparison of the fecal microbiota of two monogastric herbivorous and five omnivorous mammals

  Rana Kobayashi, Kentaro Nagaoka, Naomichi Nishimura, Satoshi Koike, Eiki Takahashi, Kimie Niimi, Harutaka Murase, Teruo Kinjo, Takamitsu Tsukahara, Ryo Inoue

  Animal Science Journal 91 (1) e13366  1344-3941 2020/04/03 [Refereed][Not invited]
  
• Occurrence and expression of genes encoding methyl-compound production in rumen bacteria.

  William J Kelly, Sinead C Leahy, Janine Kamke, Priya Soni, Satoshi Koike, Roderick Mackie, Rekha Seshadri, Gregory M Cook, Sergio E Morales, Chris Greening, Graeme T Attwood

  Animal Microbiome 1 15  2019/11/14 [Refereed][Not invited]
   

  BACKGROUND: Digestive processes in the rumen lead to the release of methyl-compounds, mainly methanol and methylamines, which are used by methyltrophic methanogens to form methane, an important agricultural greenhouse gas. Methylamines are produced from plant phosphatidylcholine degradation, by choline trimethylamine lyase, while methanol comes from demethoxylation of dietary pectins via pectin methylesterase activity. We have screened rumen metagenomic and metatranscriptomic datasets, metagenome assembled genomes, and the Hungate1000 genomes to identify organisms capable of producing methyl-compounds. We also describe the enrichment of pectin-degrading and methane-forming microbes from sheep rumen contents and the analysis of their genomes via metagenomic assembly. RESULTS: Screens of metagenomic data using the protein domains of choline trimethylamine lyase (CutC), and activator protein (CutD) found good matches only to Olsenella umbonata and to Caecibacter, while the Hungate1000 genomes and metagenome assembled genomes from the cattle rumen found bacteria within the phyla Actinobacteria, Firmicutes and Proteobacteria. The cutC and cutD genes clustered with genes that encode structural components of bacterial microcompartment proteins. Prevotella was the dominant genus encoding pectin methyl esterases, with smaller numbers of sequences identified from other fibre-degrading rumen bacteria. Some large pectin methyl esterases (> 2100 aa) were found to be encoded in Butyrivibrio genomes. The pectin-utilising, methane-producing consortium was composed of (i) a putative pectin-degrading bacterium (phylum Tenericutes, class Mollicutes), (ii) a galacturonate-using Sphaerochaeta sp. predicted to produce acetate, lactate, and ethanol, and (iii) a methylotrophic methanogen, Methanosphaera sp., with the ability to form methane via a primary ethanol-dependent, hydrogen-independent, methanogenesis pathway. CONCLUSIONS: The main bacteria that produce methyl-compounds have been identified in ruminants. Their enzymatic activities can now be targeted with the aim of finding ways to reduce the supply of methyl-compound substrates to methanogens, and thereby limit methylotrophic methanogenesis in the rumen.
• Diverse hydrogen production and consumption pathways influence methane production in ruminants

  Chris Greening, Renae Geier, Cecilia Wang, Laura C. Woods, Sergio E. Morales, Michael J. McDonald, Rowena Rushton-Green, Xochitl C. Morgan, Satoshi Koike, Sinead C. Leahy, William J. Kelly, Isaac Cann, Graeme T. Attwood, Gregory M. Cook, Roderick I. Mackie

  The ISME Journal 13 (10) 2617 - 2632 1751-7362 2019/06/26 [Refereed][Not invited]
  
• Effect of cashew nut shell liquid feeding on fermentation and microbiota in the rumen of Thai native cattle and swamp buffaloes

  S. Konda, R. Onodera, E. Kanchanasatit, P. Boonsaen, S. Sawanon, K. Nagashima, Y. Suzuki, S. Koike, Y. Kobayashi

  Livestock Science 226 99 - 106 1871-1413 2019/06/15 [Refereed][Not invited]
  
• Seasonal differences in rumen bacterial flora of wild Hokkaido sika deer and partial characterization of an unknown bacterial group possibly involved in fiber digestion in winter.

  Hidehisa Yamano, Yasuhiro Ichimura, Yoshihiko Sawabe, Satoshi Koike, Yutaka Suzuki, Yasuo Kobayashi

  Animal Science Journal 90 (6) 790 - 798 1344-3941 2019/04/14 [Refereed][Not invited]
   

  Rumen digesta was obtained from wild Hokkaido sika deer to compare bacterial flora between summer and winter. Bacterial flora was characterized with molecular-based approaches and enrichment cultivation. Bacteroidetes was shown as a major phylum followed by Firmicutes, with similar proportions in both seasons. However, two phylogenetically unique groups in Bacteroidetes were found in each season: unknown group A in winter and unknown group B in summer. The ruminal abundance of unknown group A was the highest followed by Ruminococcus flavefaciens in winter. Moreover, the abundance of these two was higher in winter than in summer. In contrast, the abundance of unknown group B was higher in summer than in winter. In addition, this group showed the highest abundance in summer among the bacteria quantified. Unknown group A was successfully enriched by cultivating with oak bark and sterilized rumen fluid, particularly that from deer. Bacteria of this group were distributed in association with the solid rather than the liquid rumen fraction, and were detected as small cocci. Accordingly, unknown group A is assumed to be involved in degradation of fibrous materials. These results suggest that wild Hokkaido sika deer develop a rumen bacterial flora in response to changes in dietary conditions.
• Selection of plant oil as a supplemental energy source by monitoring rumen profiles and its dietary application in Thai crossbred beef cattle.

  Keiji Matsuba, Apirada Padlom, Anchalee Khongpradit, Phoompong Boonsaen, Prayad Thirawong, Suriya Sawanon, Yutaka Suzuki, Satoshi Koike, Yasuo Kobayashi

  Asian-Australasian Journal of Animal Sciences 32 (10) 1511 - 1520 1011-2367 2019/02/14 [Refereed][Not invited]
   

  Objective: The present study was conducted to select a plant oil without inhibitory effects on rumen fermentation and microbes, and to determine the optimal supplementation level of the selected oil in a series of in vitro studies for dietary application. Then, the selected oil was evaluated in a feeding study using Thai crossbred beef cattle by monitoring growth, carcass, blood and rumen characteristics. Methods: Rumen fluid was incubated with substrates containing one of three different types of plant oil (coconut oil, palm oil and soybean oil) widely available in Thailand. The effects of each oil on rumen fermentation and microbes were monitored and the oil without a negative influence on rumen parameters was selected. Then, the dose-response of rumen parameters to various levels of the selected palm oil was monitored to determine a suitable supplementation level. Finally, an 8-month feeding experiment with the diet supplemented with palm oil was carried out using 12 Thai crossbred beef cattle to monitor growth, carcass, rumen and blood profiles. Results: Batch culture studies revealed that coconut and soybean oils inhibited the most potent rumen cellulolytic bacterium Fibrobacter succinogenes, while palm oil had no such negative effect on this and on rumen fermentation products at 5% or higher supplementation level. Cattle fed the diet supplemented with 2.5% palm oil showed improved feed conversion ratio (FCR) without any adverse effects on rumen fermentation. Palm oil-supplemented diet increased blood cholesterol levels, suggesting a higher energy status of the experimental cattle. Conclusion: Palm oil had no negative effects on rumen fermentation and microbes when supplemented at levels up to 5% in vitro. Thai crossbred cattle fed the palm oil-supplemented diet showed improved FCR without apparent changes of rumen and carcass characteristics, but with elevated blood cholesterol levels. Therefore, palm oil can be used as a beneficial energy source.
• Functional modulation of caecal fermentation and microbiota in rat by feeding bean husk as a dietary fibre supplement

  H. Myint, H. Kishi, Y. Iwahashi, W. Saburi, S. Koike, Y. Kobayashi

  Beneficial Microbes 9 (6) 963 - 974 1876-2883 2018/12/07 [Refereed][Not invited]
   

  A feeding study using rats was conducted to evaluate the utility of lablab bean husk and soya bean husk as sources of potential prebiotic fibre. Twenty 5-week-old Sprague Dawley rats were divided into 4 groups and fed one of the following diets for 3 weeks: purified diet (AIN93 G) containing 5% cellulose (CEL), or the same diet in which cellulose was replaced by corn starch (STA), lablab bean husk (LBH), or soya bean husk (SBH). Rats were sacrificed at 8 weeks of age and caecal digesta were collected. Feed intake, body weight, anatomical parameters, and caecal ammonia level did not differ significantly among diets. Rats on LBH and SBH showed higher concentrations of caecal short-chain fatty acid and lactate than those on CEL. Rats on CEL, SBH, and LBH exhibited lower caecal indole and skatole levels. LBH yielded increased caecal abundance of Akkermansia muciniphila and Oscillibacter relatives, as demonstrated by either qPCR, MiSeq, or clone library analysis. SBH favoured the growth of lactobacilli as assessed by both qPCR and MiSeq, and favoured the growth of bifidobacteria as assessed by MiSeq. In comparison with STA, LBH and SBH yielded lower caecal abundance of bacteria related to Dorea massiliensis, as demonstrated by qPCR, MiSeq, and clone library analysis. Both types of bean husk were found to contain oligosaccharides that might selectively stimulate the growth of beneficial bacteria. Based on these results, the two species of bean husk tested are considered potentially functional for promoting the gut health of monogastric animals.
• Cellulose acetate, a new candidate feed supplement for ruminant animals: In vitro evaluations

  Y. Watabe, Y. Suzuki, S. Koike, S. Shimamoto, Y. Kobayashi

  Journal of Dairy Science 101 (12) 10929 - 10938 0022-0302 2018/12 [Refereed][Not invited]
  
• Rumen responses to dietary supplementation with cashew nut shell liquid and its cessation in sheep

  Sungchhang Kang, Ryo Suzuki, Yutaka Suzuki, Satoshi Koike, Kyo Nagashima, Yasuo Kobayashi

  Animal Science Journal 89 (11) 1549 - 1555 1344-3941 2018/09/05 [Refereed][Not invited]
  
• Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

  Rekha Seshadri, Sinead C. Leahy, Graeme T. Attwood, Koon Hoong Teh, Suzanne C. Lambie, Adrian L. Cookson, Emiley A. Eloe-Fadrosh, Georgios A. Pavlopoulos, Michalis Hadjithomas, Neha J. Varghese, David Paez-Espino, Rechelle Perry, Gemma Henderson, Christopher J. Creevey, Nicolas Terrapon, Pascal Lapebie, Elodie Drula, Vincent Lombard, Edward Rubin, Nikos C. Kyrpides, Bernard Henrissat, Tanja Woyke, Natalia N. Ivanova, William J. Kelly, Hungate1000 project collaborators, Nikola Palevic, Peter H. Janssen, Ron S. Ronimus, Samantha Noel, Priya Soni, Kerri Reilly, Todd Atherly, Cherie Ziemer, Andre-Denis Wright, Suzanne Ishaq, Michael Cotta, Stephanie Thompson, Katie Crosley, Nest McKain, John Wallace, Harry J. Flint, Jennifer C. Martin, Robert J. Forster, Robert J. Gruninger, Tim McAllister, Rosalind Gilbert, Diane Ouwerkerk, Rosalind Gilbert, Diane Ouwerkerk, Athol Klieve, Rafat Al Jassim, Stuart Denman, Chris McSweeney, Carly Rosewarne, Satoshi Koike, Yasuo Kobayashi, Makoto Mitsumori, Takumi Shinkai, Silvio Cravero, María Cerón Cucchi

  Nature Biotechnology 36 (4) 359 - 367 1546-1696 2018/03/19 [Refereed][Not invited]
   

  Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen.
• Partial characterization of phylogeny, ecology and function of the fibrolytic bacteriumRuminococcus flavefaciens OS14, newly isolated from the rumen of swamp buffalo

  Phoompong Boonsaen, Madoka Kinjo, Suriya Sawanon, Yutaka Suzuki, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 89 (2) 377 - 385 1344-3941 2018/02 [Refereed][Not invited]
  
• Potency of cashew nut shell liquid in rumen modulation under different dietary conditions and indication of its surfactant action against rumen bacteria

  Seongjin Oh, Yasuyuki Suzuki, Shusuke Hayashi, Yutaka Suzuki, Satoshi Koike, Yasuo Kobayashi

  Journal of Animal Science and Technology 59 (1) 27 - 27 2017/11/24 [Refereed][Not invited]
   

  Background: Cashew nut shell liquid (CNSL) is an agricultural byproduct containing alkylphenols that has been shown to favorably change the rumen fermentation pattern only under experimentally fixed feeding conditions. Investigation of CNSL potency in rumen modulation under a variety of feeding regimens, and evidence leading to the understanding of CNSL action are obviously necessary for further CNSL applications. The objective of this study was to evaluate the potency of CNSL for rumen modulation under different dietary conditions, and to visually demonstrate its surfactant action against selected rumen bacteria. Methods: Batch culture studies were carried out using various diets with 5 different forage to concentrate (F:C) ratios (9:1, 7:3, 5:5. 3:7 and 1:9). Strained rumen fluid was diluted with a buffer and incubated with each diet. Gas and short chain fatty acid (SCFA) profiles were characterized after 18 h incubation at 39 °C. Monensin was also evaluated as a reference additive under the same conditions. Four species of rumen bacteria were grown in pure culture and exposed to CNSL to determine their morphological sensitivity to the surfactant action of CNSL. Results: CNSL supplementation decreased total gas production in diets with 5:5 and 3:7 F:C ratios, whereas the F:C ratio alone did not affect any gas production. Methane decrease by CNSL addition was more apparent in diets with 5:5, 3:7, and 1:9 F:C ratios. An interactive effect of CNSL and the F:C ratio was also observed for methane production. CNSL supplementation enhanced propionate production, while total SCFA production was not affected. Monensin decreased methane production but only in a diet with a 1:9 F:C ratio with increased propionate. Studies of pure cultures indicated that CNSL damaged the cell surface of hydrogen- and formate-producing bacteria, but did not change that of propionate-producing bacteria. Conclusion: CNSL can selectively inhibit rumen bacteria through its surfactant action to lead fermentation toward less methane and more propionate production. As CNSL is effective over a wider range of dietary conditions for such modulation of rumen fermentation in comparison with monensin, this new additive candidate might be applied to ruminant animals for various production purposes and at various stages.
• Plasma concentrations of glucagon-like peptide 1 and 2 in calves fed calf starters containing lactose

  Y. Inabu, A. Saegusa, K. Inouchi, S. Koike, M. Oba, T. Sugino

  Journal of Dairy Science 100 (11) 9361 - 9371 0022-0302 2017/11 [Refereed][Not invited]
   

  The objective of this study was to evaluate the effects of lactose inclusion in calf starters on plasma glucagon-like peptide (GLP)-1 and GLP-2 concentrations and gastrointestinal tract development in calves. Holstein bull calves (n = 45) were raised on an intensified nursing program using milk replacer containing 28.0% CP and 15.0% fat, and were fed a texturized calf starter containing 0 (control), 5.0 (LAC5), or 10.0% (LAC10; n = 15 for each treatment) lactose on a DM basis. Lactose was included in the starter by partially replacing dry ground corn in pelleted portion of the starter. All calf starters were formulated with 23.1% CP. The ethanol-soluble carbohydrate concentrations of the control, LAC5, and LAC10 starters were 7.3, 12.3, and 16.8% on a DM basis, respectively. Starch concentrations of the control, LAC5, and LAC10 starters were 29.7, 27.0, and 21.4% on a DM basis, respectively. All calves were fed treatment calf starters ad libitum. Blood samples were obtained weekly from 1 to 11 wk of age, and used to measure plasma GLP-1, GLP-2, and insulin concentrations, serum β-hydroxybutyrate (BHB) concentration, and blood glucose concentration. At 80 d of age, calves were euthanized, and weights of the reticulorumen, omasum, abomasum, small intestine, and large intestine tissue were measured. Serum BHB concentration was higher for calves fed the LAC10 (171 μmol/L) starter than for those fed the control (151 μmol/L) and LAC5 (145 μmol/L) starters. Plasma GLP-1 and GLP-2 concentrations did not differ between treatments. However, relative to the baseline (1 wk of age), the plasma GLP-1 concentration was higher for the LAC10 (125.9%) than for the LAC5 (68.2%) and control (36.8%), and for the LAC5 than for the control (36.8%). Moreover, similar differences between treatments were observed for GLP-2 concentration relative to the baseline (88.2, 76.9, and 74.9% for LAC10, LAC5, and control treatments, respectively). The serum BHB concentration was positively correlated with the plasma GLP-1 concentration (r = 0.428). Furthermore, the plasma GLP-1 concentration was positively correlated with the insulin concentration (r = 0.793). The weights of the reticulorumen, omasum, abomasum, small intestine, and large intestine were not affected by the treatments. In conclusion, inclusion of lactose in calf starters resulted in higher plasma GLP-1 and GLP-2 concentrations, and BHB might be associated with higher plasma GLP-1 concentration.
• Effect of soybean husk supplementation on the fecal fermentation metabolites and microbiota of dogs

  Htun Myint, Yu Iwahashi, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 88 (11) 1730 - 1736 1344-3941 2017/11 [Refereed][Not invited]
  
• Effect of ginkgo extract supplementation on in vitro rumen fermentation and bacterial profiles under different dietary conditions

  Seongjin Oh, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 88 (11) 1737 - 1743 1344-3941 2017/11 [Refereed][Not invited]
   

  Ginkgo extract was applied to a batch culture study and evaluated for its potential as a feed additive for ruminant animals under different forage-to-concentrate (F:C) ratios (1:9, 3:7, 5:5, 7:3 and 9:1). Rumen fluid was mixed with respective diet and incubated at 39 degrees C for 24h with and without ginkgo extract (1.6% fruit equivalent in culture). Methane production was significantly decreased by ginkgo extract, with the greatest reductions found in the 5:5 (41.9%) followed by the 7:3 ratios (36.7%). Total short chain fatty acid and ammonia levels were not affected by ginkgo extract supplementation in any of the five different diets. However, ginkgo extract increased propionate proportion and decreased acetate proportion in all dietary conditions tested. The levels of total bacteria, Ruminococcus flavefaciens, Ruminococcus albus and Fibrobacter succinogenes were decreased by ginkgo extract. The levels of Selenomonas ruminantium, Anaerovibrio lipolytica, Ruminobacter amylophilus, Succinivibrio dextrinosolvens and Megasphaera elsdenii were increased by ginkgo extract supplementation, possibly contributing to the higher propionate production. These results suggest that rumen modulation by ginkgo extract can be achieved at a wide range of F:C ratios with no adverse impact on feed digestion. Moreover, F:C ratios of 5:5 and 7:3 may be optimal when methane mitigation is expected.
• Potency of ginkgo fruit for modulation of rumen microbiota and fermentation

  OH Seongjin, SUZUKI Yutaka, KOIKE Satoshi, KOBAYASHI Yasuo

  栄養生理研究会報 家畜栄養生理研究会 61 (2) 33‐41 - 41 0286-4754 2017/09 [Refereed][Invited]
  
• Bean husk, an agricultural by-product having functionality in animal nutrition and health

  MYINT Htun, KISHI Hiroyuki, IWAHASHI Yu, SUZUKI Yutaka, KOIKE Satoshi, KOBAYASHI Yasuo

  栄養生理研究会報 家畜栄養生理研究会 61 (2) 13‐19 - 19 0286-4754 2017/09 [Refereed][Invited]
  
• Effects of partial replacement of corn grain with lactose in calf starters on ruminal fermentation and growth performance

  A. Saegusa, K. Inouchi, M. Ueno, Y. Inabu, S. Koike, T. Sugino, M. Oba

  Journal of Dairy Science 100 (8) 6177 - 6186 0022-0302 2017/08 [Refereed][Not invited]
   

  The objective of this study was to evaluate effects of partial replacement of dry ground corn with lactose in calf starters on dry matter intake, growth rate, ruminal pH, and volatile fatty acid profile. Sixty Holstein bull calves were raised on a high plane of nutrition program until 55 d of age. Calves were fed texturized calf starters containing 30.1% steam-flaked grains and lactose at 0 (control), 5, or 10% (n = 20 for each treatment) on a dry matter basis. All calves were fed treatment calf starters ad libitum from d 7 and kleingrass hay from d 35. Ruminal pH was measured continuously immediately after weaning (d 55–62) for 15 calves (n = 5 per treatment), and 3 wk after weaning (d 77 to 80) for the other 45 calves (n = 15 per treatment). Dry matter intake, growth performance, and ruminal pH variables were not affected by treatment. However, according to Spearman's correlation coefficient (rs) analyses, lactose intake was positively correlated with dairy minimum ruminal pH (rs = 0.306) for the data collected from d 77 to 80. Similarly, hay intake was not affected by treatment, but positively correlated with daily mean (rs = 0.338) and maximum ruminal pH (rs = 0.408) and negatively correlated with duration pH <5.8 (rs = −0.329) and area pH <5.8 (rs = −0.325), indicating that the variation in hay intake among animals might have masked treatment effects on ruminal pH. Ruminal molar ratio of acetate was higher (45.2 vs. 40.6%), and that of propionate was lower in 10% lactose than control (35.3 vs. 40.2%) for ruminal fluid collected on d 80; however, molar ratio of butyrate was not affected by treatment. These results indicate that lactose inclusion in calf starters up to 10% of dry matter might not affect dry matter intake and growth performance of calves, but that greater lactose and hay intake might be associated with higher ruminal pH.
• Ginkgo fruit extract as an additive to modify rumen microbiota and fermentation and to mitigate methane production

  S. Oh, R. Shintani, S. Koike, Y. Kobayashi

  Journal of Dairy Science 100 (3) 1923 - 1934 0022-0302 2017/03 [Refereed][Not invited]
   

  Ginkgo fruit, an unused byproduct of the ginkgo nut industry, contains antimicrobial compounds known as anacardic acids. Two major cultivars of ginkgo, Kyuju (K) and Tokuro (T), were evaluated for their potential as a feed additive for ruminants. In batch culture, we incubated a mixture of hay and concentrate in diluted rumen fluid with or without 1.6% (fruit equivalent) ginkgo fruit extract. We conducted another series of batch culture studies to determine the dose response of fermentation. We also conducted continuous culture using the rumen simulation technique (RUSITEC) with cultivar K and carried out a pure culture study to monitor the sensitivity of 17 representative rumen bacterial species to ginkgo extract and component phenolics. Although both K and T extracts led to decreased methane and increased propionate production, changes were more apparent with K extract, and were dose-dependent. Total gas production was depressed at doses >= 3.2%, suggesting that 1.6% was the optimal supplementation level. In RUSITEC fermentation supplemented with 1.6% ginkgo K, methane decreased by 53% without affecting total gas or total VFA production, but with decreased acetate and increased propionate. Disappearance of dry matter, neutral detergent fiber, and acid detergent fiber were not affected by ginkgo, but ammonia levels were decreased. Quantitative PCR indicated that the abundance of protozoa, fungi, methanogens, and bacteria related to hydrogen and formate production decreased, but the abundance of bacteria related to propionate production increased. MiSeq analysis (Illumina Inc., San Diego, CA) confirmed these bacterial changes and identified archaeal community changes, including a decrease in Methanobrevibacter and Methanomassiliicoccaceae and an increase in Methanoplanus. Pure culture study results supported the findings for the above bacterial community changes. These results demonstrate that ginkgo fruit can modulate rumen fermentation toward methane mitigation and propionate enhancement via microbial selection.
• Effect of chickpea husk dietary supplementation on blood and cecal parameters in rats

  Htun Myint, Hiroyuki Kishi, Satoshi Koike, Yasuo Kobayashi

  Animal Science Journal 88 (2) 372 - 378 1344-3941 2017/02 [Refereed][Not invited]
   

  Chickpea husk was functionally evaluated for antioxidant status, blood parameters, cecal fermentation and microbial profiles in rats. Fifteen male rats (5 weeks of age) were divided into three groups; they were individually housed and fed one of the following diets for 3 weeks: purified diet containing 5% cellulose (Cellulose), an identical diet in which cellulose was replaced by corn starch (Starch) or by chickpea husk (Chick). Rats were sacrificed to obtain blood and cecal digesta samples. Chickpea husk contained high polyphenolic content and significant superoxide dismutase and 2,2-diphenyl-picrylhydrazyl scavenging activities. In a feeding experiment, Chick showed lowered cholesterol levels and improved antioxidant activity represented by reduced thiobarbituric acid reactive substances in blood. Chick showed increased cecal levels of total short chain fatty acids and butyrate, leading to a lower pH. Chick presented with lowered cecal indole and skatole concentrations, as did Cellulose. Cecal bacterial changes were notable in Chick, evidenced by differences in denaturing gradient gel electrophoresis banding patterns. However, representative bacteria quantified by real-time PCR assay did not support this bacterial change. These results indicate that chickpea husk feeding can improve the antioxidative status of rats through its polyphenolic components and modulate the hindgut environment by its fibrous components.
• Use of Asian selected agricultural byproducts to modulate rumen microbes and fermentation

  Yasuo Kobayashi, Seongjin Oh, Htun Myint, Satoshi Koike

  Journal of Animal Science and Biotechnology 7 (1) 2049-1891 2016/12 [Refereed][Invited]
   

  In the last five decades, attempts have been made to improve rumen fermentation and host animal nutrition through modulation of rumen microbiota. The goals have been decreasing methane production, partially inhibiting protein degradation to avoid excess release of ammonia, and activation of fiber digestion. The main approach has been the use of dietary supplements. Since growth-promoting antibiotics were banned in European countries in 2006, safer alternatives including plant-derived materials have been explored. Plant oils, their component fatty acids, plant secondary metabolites and other compounds have been studied, and many originate or are abundantly available in Asia as agricultural byproducts. In this review, the potency of selected byproducts in inhibition of methane production and protein degradation, and in stimulation of fiber degradation was described in relation to their modes of action. In particular, cashew and ginkgo byproducts containing alkylphenols to mitigate methane emission and bean husks as a source of functional fiber to boost the number of fiber-degrading bacteria were highlighted. Other byproducts influencing rumen microbiota and fermentation profile were also described. Future application of these feed and additive candidates is very dependent on a sufficient, cost-effective supply and optimal usage in feeding practice.
• Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range

  Gemma Henderson, Faith Cox, Siva Ganesh, Arjan Jonker, Wayne Young, Peter H. Janssen

  Scientific Reports 5 (1) 2045-2322 2015/11/26 [Refereed][Not invited]
   

  Ruminant livestock are important sources of human food and global greenhouse gas emissions. Feed degradation and methane formation by ruminants rely on metabolic interactions between rumen microbes and affect ruminant productivity. Rumen and camelid foregut microbial community composition was determined in 742 samples from 32 animal species and 35 countries, to estimate if this was influenced by diet, host species, or geography. Similar bacteria and archaea dominated in nearly all samples, while protozoal communities were more variable. The dominant bacteria are poorly characterised, but the methanogenic archaea are better known and highly conserved across the world. This universality and limited diversity could make it possible to mitigate methane emissions by developing strategies that target the few dominant methanogens. Differences in microbial community compositions were predominantly attributable to diet, with the host being less influential. There were few strong co-occurrence patterns between microbes, suggesting that major metabolic interactions are non-selective rather than specific.
• Monitoring of gene expression in Fibrobacter succinogenes S85 under the co-culture with non-fibrolytic ruminal bacteria

  Naoki M. Fukuma, Satoshi Koike, Yasuo Kobayashi

  Archives of Microbiology Springer 197 (2) 269 - 276 0302-8933 2015/03 [Refereed][Not invited]
   

  Fibrobacter succinogenes is one of the most pivotal fibrolytic bacterial species in the rumen. In a previous study, we confirmed enhancement of fiber digestion in a co-culture of F. succinogenes S85 with non-fibrolytic ruminal strains R-25 and/or Selenomonas ruminantium S137. In the present study, mRNA expression level of selected functional genes in the genome of F. succinogenes S85 was monitored by real-time RT-PCR. Growth profile of F. succinogenes S85 was similar in both the monoculture and co-cultures with non-fibrolytics. However, expression of 16S rRNA gene of F. succinogenes S85 in the co-culture was higher (P < 0.01) than that of the monoculture. This finding suggests that metabolic activity of F. succinogenes S85 was enhanced by coexistence with strains R-25 and/or S. ruminantium S137. The mRNA expression of fumarate reductase and glycoside hydrolase genes was up-regulated (P < 0.01) when F. succinogenes S85 was co-cultured with non-fibrolytics. These results indicate the enhancement of succinate production and fiber hydrolysis by F. succinogenes S85 in co-cultures of S. ruminantium and R-25 strains.
• Interaction of rumen bacteria as assumed by colonization patterns on untreated and alkali-treated rice straw

  Koike, S., Yabuki, H., Kobayashi, Y.

  Animal Science Journal 85 (5) 524 - 531 1344-3941 2014/05 [Refereed][Not invited]
  
• Determination of bacteria constituting ruminal fibrolytic consortia developed on orchard grass hay stem

  Shinkai, T., Ueki, T., Koike, S., Kobayashi, Y.

  Animal Science Journal 85 (3) 254 - 261 1344-3941 2014/03 [Refereed][Not invited]
  
• Phenotypic and genotypic characterization of antibiotic-resistant soil and manure bacteria adjacent to swine production facilities

  Ekizoglu, M., Koike, S., Krapac, I., Sultan, M.N., Mackie, R.

  Turkish Journal of Veterinary and Animal Sciences 37 (5) 504 - 511 1300-0128 2013/08 [Refereed][Not invited]
  
• Involvement of recently cultured group U2 bacterium in ruminal fiber digestion revealed by coculture with Fibrobacter succinogenes S85

  Fukuma, N., Koike, S., Kobayashi, Y.

  FEMS Microbiology Letters 336 (1) 17 - 25 0378-1097 2012/11 [Refereed][Not invited]
  
• Use of bean husk as an easily digestible fiber source for activating the fibrolytic rumen bacterium Fibrobacter succinogenes and rice straw digestion

  Fuma, R., Oyaizu, S., Nukui, Y., Ngwe, T., Shinkai, T., Koike, S., Kobayashi, Y.

  Animal Science Journal 83 (10) 696 - 703 1344-3941 2012/10 [Refereed][Not invited]
  
• Bean husks as a supplemental fiber for ruminants: Potential use for activation of fibrolytic rumen bacteria to improve main forage digestion

  Ngwe, T., Nukui, Y., Oyaizu, S., Takamoto, G., Koike, S., Ueda, K., Nakatsuji, H., Kondo, S., Kobayashi, Y.

  Animal Science Journal 83 (1) 43 - 49 1344-3941 2012/01 [Refereed][Not invited]
  
• Agricultural by-products as modulators of rumen microbiota

  Kobayashi Y, Shinkai T, Koike S

  International Colloquium on Rumen Microbiology 49 - 60 2012 [Refereed][Invited]
  
• Evidence for the possible involvement of Selenomonas ruminantium in rumen fiber digestion

  Sawanon, S., Koike, S., Kobayashi, Y.

  FEMS Microbiology Letters 325 (2) 170 - 179 0378-1097 2011/12 [Refereed][Not invited]
  
• Effect of liquid whey feeding on fecal microbiota of mature and growing pigs

  Yasuo KOBAYASHI, Aya ITOH, Kanae MIYAWAKI, Satoshi KOIKE, Osamu IWABUCHI, Yuji IIMURA, Yuri KOBASHI, Tomoyuki KAWASHIMA, Junichi WAKAMATSU, Akihito HATTORI, Hiroshi MURAKAMI, Fumiki MORIMATSU, Takashi NAKAEBISU, Takeshi HISHINUMA

  Animal Science Journal Blackwell Publishing 82 (4) 607 - 615 1344-3941 2011/08 [Refereed][Not invited]
   

  The effect of liquid whey feeding on fecal bacteria and their metabolites was assessed in five pregnant sows and 66 growing pigs. Sows were fed a control diet for 4 weeks (control period) followed by the same diet but with whey feeding (5 L/day/pig) for 4 weeks (whey period). One group of growing pigs was given 267 L of whey per pig (whey group), while the other group was not (control group). In both cases, liquid whey was given separately from control diet. Sows in the whey period had feces showing lower pH, lower ammonia concentration, and larger population sizes of total bacteria, lactobacilli, and bifidobacteria. The bacterial gene library analysis indicated that Mitsuokella and Megasphaera were more frequently detected, while Clostridium disporicum were detected less frequently in the whey period. Feces from whey-fed growing pigs showed lower pH than that from control pigs in the early stage of growing. Also, larger populations of total bacteria, lactobacilli, and bifidobacteria were recorded in the whey group. From the analysis of bacterial gene library, the detection frequency of Lactobacillus reuteri tended to be higher in the whey group. These results indicate that whey feeding influences the hindgut microbiota of pigs, possibly leading to a fermentation shift that is favorable for animal health.
• Phylogenetic diversity and dietary association of rumen Treponema revealed using group-specific 16S rRNA gene-based analysis

  Aschalew Z. Bekele, Satoshi Koike, Yasuo Kobayashi

  FEMS Microbiology Letters Blackwell Publishing 316 (1) 51 - 60 0378-1097 2011/03 [Refereed][Not invited]
   

  Treponema spp. are a commonly detected bacterial group in the rumen that are involved in the degradation of soluble fibers. In this study, a ruminal Treponema group-specific PCR primer targeting the 16S rRNA gene was designed and used to assess the phylogenetic diversity and diet association of this group in sheep rumen. Total DNA was extracted from rumen digesta of three sheep fed a diet based on alfalfa/orchardgrass hay or concentrate. The real-time PCR quantification indicated that the relative abundance of the Treponema group in the total rumen bacteria was as high as 1.05%, while the known species Treponema bryantii accounted for only 0.02%. Fingerprints of the Treponema community determined by 16S rDNA-targeted denaturing gradient gel electrophoresis (DGGE) analysis tended to differ among the diets. Principal component analysis of the DGGE profiles distinguished those Treponema associated with either the hay or the concentrate diets. Analysis of a Treponema 16S rRNA gene clone library showed phylogenetically distinct operational taxonomic units for a specific dietary condition, and significant (P=0.001) differences in community composition were observed among clone libraries constructed from each dietary regimen. The majority of clones (75.4%) had less than 97% sequence similarity with known Treponema. These results suggest the predominance of uncultured Treponema that appear to have distinct members related to the digestion of either hay or concentrate diet.
• In vitro evaluation of cashew nut shell liquid as a methane-inhibiting and propionate-enhancing agent for ruminants

  Watanabe, Y., Suzuki, R., Koike, S., Nagashima, K., Mochizuki, M., Forster, R.J., Kobayashi, Y.

  Journal of Dairy Science 93 (11) 5258 - 5267 0022-0302 2010/11 [Refereed][Not invited]
  
• Molecular ecology of macrolide-lincosamide-streptogramin B methylases in waste lagoons and subsurface waters associated with swine production

  Koike, S., Aminov, R.I., Yannarell, A.C., Gans, H.D., Krapac, I.G., Chee-Sanford, J.C., Mackie, R.I.

  Microbial Ecology 59 (3) 487 - 498 0095-3628 2010/04 [Refereed][Not invited]
  
• Molecular Monitoring and Isolation of Previously Uncultured Bacterial Strains from the Sheep Rumen

  S. Koike, Y. Handa, H. Goto, K. Sakai, E. Miyagawa, H. Matsui, S. Ito, Y. Kobayashi

  Applied and Environmental Microbiology American Society for Microbiology 76 (6) 1887 - 1894 0099-2240 2010/03/15 [Refereed][Not invited]
   

  To estimate the contribution of uncultured bacterial groups to fiber degradation, we attempted to retrieve both ecological and functional information on uncultured groups in the rumen. Among previously reported uncultured bacteria, fiber-associated groups U2 and U3, belonging to the low-GC Gram-positive bacterial group, were targeted. PCR primers and fluorescence in situ hybridization (FISH) probe targeting 16S rRNA genes or rRNA were designed and used to monitor the distribution of targets. The population size of group U2 in the rumen was as high as 1.87%, while that of group U3 was only 0.03%. Strong fluorescence signals were observed from group U2 cells attached to plant fibers in the rumen. These findings indicate the ecological significance of group U2 in the rumen. We succeeded in enriching group U2 using rumen-incubated rice straw as the inoculum followed by incubation in an appropriate medium with an agent inhibitory for Gram-negative bacteria. Consequently, we successfully isolated two strains, designated B76 and R-25, belonging to group U2. Both strains were Gram-positive short rods or cocci that were 0.5 to 0.8 μm in size. Strain B76 possessed xylanase and α- l -arabinofuranosidase activity. In particular, the xylanase activity of strain B76 was higher than that of xylanolytic Butyrivibrio fibrisolvens H17c grown on cellobiose. Strain R-25 showed an α- l -arabinofuranosidase activity higher than that of strain B76. These results suggest that strains B76 and R-25 contribute to hemicellulose degradation in the rumen.
• Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis

  Aschalew Z. Bekele, Satoshi Koike, Yasuo Kobayashi

  FEMS Microbiology Letters Blackwell Publishing 305 (1) 49 - 57 0378-1097 2010/03/04 [Refereed][Not invited]
   

  16S rDNA-based analysis of rumen Prevotella was carried out to estimate the diversity and diet specificity of bacteria belonging to this genus. Total DNA was extracted from rumen digesta of three sheep fed two diets with different hay-to-concentrate ratios (10:1 and 1:2). Real-time PCR quantification of Prevotella revealed that the relative abundance of this genus in total rumen bacteria was up to 19.7%, while the representative species Prevotella bryantii and Prevotella ruminicola accounted for only 0.6% and 3.8%, respectively. Denaturing gradient gel electrophoresis analysis for Prevotella revealed shifts in community composition with diet. Analysis of 16S rDNA clone libraries showed significant differences (P=0.001) between clones detected from the sheep on the diets with different hay-to-concentrate ratios. The majority (87.8%) of Prevotella clones had < 97% sequence similarity with known rumen Prevotella. These data suggest that uncultured Prevotella is more abundant than known Prevotella and that members of this genus appear to have specific metabolic niches.
• Molecular Analyses of an Unusual Translesion DNA Polymerase from Methanosarcina acetivorans C2A

  Li-Jung Lin, Aya Yoshinaga, Yuyen Lin, Claudia Guzman, Yi-Hsing Chen, Shou Mei, Angelica M. Lagunas, Satoshi Koike, Shigenori Iwai, M. Ashley Spies, Satish K. Nair, Roderick I. Mackie, Yoshizumi Ishino, Isaac K.O. Cann

  Journal of Molecular Biology Elsevier 397 (1) 13 - 30 0022-2836 2010/03 [Refereed][Not invited]
  
• Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste

  Chee-Sanford, J.C., Mackie, R.I., Koike, S., Krapac, I.G., Lin, Y.-F., Yannarell, A.C., Maxwell, S., Aminov, R.I.

  Journal of Environmental Quality 38 (3) 1086 - 1108 0047-2425 2009/05 [Refereed][Not invited]
  
• Fibrolytic Rumen Bacteria: Their Ecology and Functions

  Satoshi Koike, Yasuo Kobayashi

  ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 22 (1) 131 - 138 1011-2367 2009/01 [Not refereed][Invited]
   

  Among rumen microbes, bacteria play important roles in the biological degradation of plant fiber due to their large biomass and high activity. To maximize the utilization of fiber components such as cellulose and hemicellulose by ruminant animals, the ecology and functions of rumen bacteria should be understood in detail. Recent genome sequencing analyses of representative fibrolytic bacterial species revealed that the number and variety of enzymes for plant fiber digestion clearly differ between Fibrobacter succinogenes and Ruminococcus flavefaciens. Therefore, the mechanism of plant fiber digestion is also thought to differ between these two species. Ecology of individual fibrolytic bacterial species has been investigated using pure cultures and electron microscopy. Recent. advances in molecular biology techniques complement the disadvantages of conventional techniques and allow accurate evaluation of the ecology of specific bacteria in mixed culture, even in situ and in vivo. Molecular monitoring of fibrolytic bacterial species in the: rumen indicated the predominance of F succinogenes. Nutritive interactions between fibrolytic and non-fibrolytic bacteria are important in maintaining and promoting fibrolytic activity, mainly in terms of crossfeeding of metabolites. Recent 16S rDNA-based analyses suggest that presently recognized fibrolytic species such as F succinogenes and two Ruminococcus species with fibrolytic activity may represent only a small proportion of the total fibrolytic population and that uncultured bacteria may be responsible for fiber digestion in the rumen. Therefore, characterization of these unidentified bacteria is important to fully understand the physiology and ecology of fiber digestion. To achieve this, a combination of conventional and modern techniques could be useful.
• Ecological and physiological characterization shows that Fibrobacter succinogenes is important in rumen fiber digestion - Review

  Kobayashi, Y., Shinkai, T., Koike, S.

  Folia Microbiologica 53 (3) 195 - 200 0015-5632 2008/05 [Refereed][Invited]
  
• Phylogenetic analysis of hindgut microbiota in Hokkaido native horses compared to light horses

  Hidehisa YAMANO, Satoshi KOIKE, Yasuo KOBAYASHI, Hiroshi HATA

  Animal Science Journal 79 (2) 234 - 242 1344-3941 2008/04 [Refereed][Not invited]
  
• Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period

  Koike, S., Krapac, I.G., Oliver, H.D., Yannarell, A.C., Chee-Sanford, J.C., Aminov, R.I., Mackie, R.I.

  Applied and Environmental Microbiology 73 (15) 4813 - 4823 0099-2240 2007/08 [Refereed][Not invited]
   

  To monitor the dissemination of resistance genes into the environment, we determined the occurrence of tetracycline resistance (Tc ^r ) genes in groundwater underlying two swine confinement operations. Monitoring well networks (16 wells at site A and 6 wells at site C) were established around the lagoons at each facility. Groundwater ( n = 124) and lagoon ( n = 12) samples were collected from the two sites at six sampling times from 2000 through 2003. Total DNA was extracted, and PCR was used to detect seven Tc ^r genes [ tet (M), tet (O), tet (Q), tet (W), tet (C), tet (H), and tet (Z)]. The concentration of Tc ^r genes was quantified by real-time quantitative PCR. To confirm the Tc ^r gene source in groundwater, comparative analysis of tet (W) gene sequences was performed on groundwater and lagoon samples. All seven Tc ^r genes were continually detected in groundwater during the 3-year monitoring period at both sites. At site A, elevated detection frequency and concentration of Tc ^r genes were observed in the wells located down-gradient of the lagoon. Comparative analysis of tet (W) sequences revealed that the impacted groundwater contained gene sequences almost identical (99.8% identity) to those in the lagoon, but these genes were not found in background libraries. Novel sequence clusters and unique indigenous resistance gene pools were also found in the groundwater. Thus, antibiotic resistance genes in groundwater are affected by swine manure, but they are also part of the indigenous gene pool.
• Validation and application of real-time polymerase chain reaction assays for representative rumen bacteria

  Satoshi KOIKE, Hiroyoshi YABUKI, Yasuo KOBAYASHI

  Animal Science Journal 78 (2) 135 - 141 1344-3941 2007/04 [Refereed][Not invited]
  
• Tetracycline residues and tetracycline resistance genes in groundwater impacted by swine production facilities

  MacKie, R.I., Koike, S., Krapac, I., Chee-Sanford, J., Maxwell, S., Aminov, R.I.

  Animal Biotechnology 17 (2) 157 - 176 1049-5398 2006/12 [Refereed][Not invited]
  
• Hindgut microbes, fermentation and their seasonal variations in Hokkaido native horses compared to light horses

  Yasuo Kobayashi, Satoshi Koike, Makoto Miyaji, Hiroshi Hata, Keiichi Tanaka

  Ecological Research Springer 21 (2) 285 - 291 0912-3814 2006/03 [Refereed][Not invited]
   

  Fecal bacteria and protozoa of Hokkaido native horses and light horses were enumerated to compare seasonal variation in hindgut microbes and fermentation between the two breeds. Fecal samples were collected in winter and summer from eight horses (four for each breed) that had been reared together under the same conditions after birth (on woodland pasture in winter and on grassland pasture for the rest of the year). Total fecal bacteria counts for both breeds showed temporal variation, with the highest levels occurring in summer (P<0.05). For both breeds, Gram-negative rods were the major constituents (58–69%) and showed higher counts in winter (P<0.05) than in summer. Total protozoa counts in both breeds were lower in winter than in summer (P<0.05). The proportion of large cellulolytic protozoa such as Cochliatoxum periachtum was increased (P<0.05) in winter, and this tended to be more pronounced in native horses. Although total volatile fatty acids (VFA) in feces were lower in winter (P<0.05), the reduction was smaller in native horses (P<0.05). Fecal VFA pattern showed a shift toward more acetate and less propionate production in winter regardless of the horse breed. Evaluation of digestive tract organs in 12 animals showed that the relative weight of the colon in body weight or total digestive tract weight is larger in native horses than in light horses (P<0.05). The present results suggest that hindgut microbial adaptation to winter diets occurs to a greater extent in native horses, as partly characterized by advantages in anatomy.
• Ruminal distribution of the cellulolytic bacterium Fibrobacter succinogenes in relation to its phylogenetic grouping

  Satoshi KOIKE, Jun PAN, Tomoyuki SUZUKI, Toru TAKANO, Chihiro OSHIMA, Yasuo KOBAYASHI, Keiichi TANAKA

  Animal Science Journal 75 (5) 417 - 422 1344-3941 2004/10 [Refereed][Not invited]
  
• Molecular microbial ecology of the gastrointestinal tract: from phylogeny to function.

  Erwin G Zoetendal, Biao Cheng, Satoshi Koike, Roderick I Mackie

  Current issues in intestinal microbiology 5 (2) 31 - 47 1466-531X 2004/09 [Refereed][Not invited]
   

  During the past decade it became evident that anaerobic cultivation-based approaches provides an incomplete picture of the microbial diversity in the GI tract, since at present only a minority of microbes can be obtained in culture. The application of molecular, mainly 16S ribosomal RNA (rRNA)-based approaches enables researchers to bypass the cultivation step and has proven its usefulness in studying the microbial composition in a variety of ecosystems, including the gastrointestinal (GI) tract. This critical review summarizes the impact of these culture-independent approaches on our knowledge of the ecology of the GI tract and provides directions for future studies which should emphasize function of specific strains, species and groups of microbes.
• Partial characterization of structure and function of a xylanase gene from the rumen hemicellulolytic bacterium Eubacterium ruminantium

  Hidenori TAGUCHI, Satoshi KOIKE, Yasuo KOBAYASHI, Isaac K. O. CANN, Shuichi KARITA

  Animal Science Journal 75 (4) 325 - 332 1344-3941 2004/08 [Refereed][Not invited]
  
• Rumen microbes and fermentation of wild sika deer on the Shiretoko peninsula of Hokkaido Island, Japan

  Yasuhiro ICHIMURA, Hidehisa YAMANO, Toru TAKANO, Satoshi KOIKE, Yasuo KOBAYASHI, Keiichi TANAKA, Nobuo OZAKI, Masatsugu SUZUKI, Hideaki OKADA, Masami YAMANAKA

  Ecological Research Springer 19 (4) 389 - 395 0912-3814 2004/07 [Refereed][Not invited]
  
• Effect of ammonia treatment on physical strength of rice straw, distribution of straw particles and particle-associated bacteria in sheep rumen

  Selim, A.S.M., Pan, J., Takano, T., Suzuki, T., Koike, S., Kobayashi, Y., Tanaka, K.

  Animal Feed Science and Technology 115 (1-2) 117 - 128 0377-8401 2004/07 [Refereed][Not invited]
  
• Recent advances in gut microbiology and their possible contribution to animal health and production - A review

  Kobayashi, Y., Koike, S., Taguchi, H., Itabashi, H., Kam, D.K., Ha, J.K.

  Asian-Australasian Journal of Animal Sciences 17 (6) 877 - 884 1011-2367 2004/06/01 [Refereed][Invited]
  
• Molecular ecological analysis of the gastrointestinal microbiota: A review

  EG Zoetendal, CT Collier, S Koike, RI Mackie, HR Gaskins

  JOURNAL OF NUTRITION 134 (2) 465 - 472 0022-3166 2004/02 [Not refereed][Invited]
   

  The gastrointestinal (GI) microbiota of mammals is characterized by its high population density, wide diversity and complexity of interactions. While all major groups of microbes are represented, bacteria predominate. Importantly, bacterial cells outnumber animal (host) cells by a factor of ten and have a profound influence on nutritional, physiological and immunological processes in the host animal. Our knowledge of the molecular and cellular bases of host-microbe interactions is limited, though critically needed to determine if and how the GI microbiota contributes to various enteric disorders in humans and animals. Traditionally, GI bacteria have been studied via cultivation-based techniques, which are labor intensive and require previous knowledge of individual nutritional and growth requirements. Recently, findings from culture-based methods have been supplemented with molecular ecology techniques that are based on the 16S rRNA gene. These techniques enable characterization and quantification of the microbiota, while also providing a classification scheme to predict phylogenetic relationships. The choice of a particular molecular-based approach depends on the questions being addressed. Clone libraries can be sequenced to identify the composition of the microbiota, often to the species level. Microbial community structure can be analyzed via fingerprinting techniques, while dot blot hybridization or fluorescent in situ hybridization can measure abundance of particular taxa. Emerging approaches, such as those based on functional genes and their expression and the combined use of stable isotopes and biomarkers, are being developed and optimized to study metabolic activities of groups or individual organisms in situ. Here, a critical summary is provided of current molecular ecological approaches for studying the GI microbiota.
• Molecular detection of verotoxigenic Escherichia coli (VTEC) from animal feces for screening VTEC-shedders

  Kobayashi, Y., Sato, M., Taguchi, H., Koike, S., Nakatsuji, H., Tanaka, K.

  Asian-Australasian Journal of Animal Sciences 17 (3) 423 - 427 1011-2367 2004/01/01 [Refereed][Not invited]
  
• Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria

  Koike, S., Yoshitani, S., Kobayashi, Y., Tanaka, K.

  FEMS Microbiology Letters 229 (1) 23 - 30 0378-1097 2003/12 [Refereed][Not invited]
  
• Expression and export of aRuminococcus albuscellulase inButyrivibrio fibrisolvensthrough the use of an alternative gene promoter and signal sequence

  Yasuo Kobayashi, Hidenori Taguchi, Takashi N Goto, Satoshi Koike, Kunio Ohmiya

  Canadian Journal of Microbiology 49 (6) 375 - 382 0008-4166 2003/06/01 [Refereed][Not invited]
   

  Ruminococcal cellulase (Ruminococcus albus F-40 endoglucanase EgI) was successfully expressed in Butyrivibrio fibrisolvens OB156C, using the erm promoter from pAMβ1. A newly identified signal peptide coding region of xynA from B. fibrisolvens 49 allowed efficient translocation of the foreign EgI into the extracellular fraction. First, B. fibrisolvens xynA with or without its own putative signal peptide (XynA SP) coding region was cloned into a shuttle vector to transform B. fibrisolvens OB156C. Both plasmids caused a 2- to 2.4-fold increase in xylanase activity. The transformant expressing XynA with the signal peptide showed a significantly higher proportion of activity in the extracellular fraction than the transformant with XynA lacking the signal peptide (75% vs. 19%), demonstrating the significance of XynA SP in the translocation of the expressed enzyme. Second, using the XynA SP coding region, secretion of EgI was attempted in B. fibrisolvens. Since the signal peptide of R. albus EgI did not function in B. fibrisolvens, it was replaced with the XynA SP. A high activity variant of EgI containing the XynA SP was transcribed using the erm promoter, resulting in a 27-fold increase in endoglucanase activity, most of which (>93%) was in the extracellular fraction of the B. fibrisolvens transformant. EgI without the XynA SP was scarcely detected in the extracellular fraction (<10%).Key words: Butyrivibrio fibrisolvens, Ruminococcus albus, cellulase, gene promoter, signal peptide.
• Effect of mastication on degradation of orchardgrass hay stem by rumen microbes: Fibrolytic enzyme activities and microbial attachment

  Pan, J., Koike, S., Suzuki, T., Ueda, K., Kobayashi, Y., Tanaka, K., Okubo, M.

  Animal Feed Science and Technology 106 (1-4) 69 - 79 0377-8401 2003/04 [Refereed][Not invited]
  
• Kinetics of In Sacco Fiber-Attachment of Representative Ruminal Cellulolytic Bacteria Monitored by Competitive PCR

  S. Koike, J. Pan, Y. Kobayashi, K. Tanaka

  Journal of Dairy Science 86 (4) 1429 - 1435 0022-0302 2003/04 [Refereed][Not invited]
  
• Effects of urea infused into the rumen on liquid- and particle-associated fibrolytic enzyme activities in steers fed low quality grass hay

  Pan, J., Suzuki, T., Koike, S., Ueda, K., Kobayashi, Y., Tanaka, K., Okubo, M.

  Animal Feed Science and Technology 104 (1-4) 13 - 27 0377-8401 2003/02 [Refereed][Not invited]
  
• Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens

  Satoshi Koike, Yasuo Kobayashi

  FEMS Microbiology Letters 204 (2) 361 - 366 0378-1097 2001/11 [Refereed][Not invited]
  
• Fecal Bacteria in Hokkaido Native Horses as Characterized by Microscopic Enumeration and Competitive Polymerase Chain Reaction Assays.

  Satoshi KOIKE, Yuko SHINGU, Hiroyuki INABA, Masahito KAWAI, Yasuo KOBAYASHI, Hiroshi HATA, Keiichi TANAKA, Masahiko OKUBO

  Journal of Equine Science Japanese Society of Equine Science 11 (2) 45 - 50 1340-3516 2000 [Refereed][Not invited]
   

  Fecal bacteria in Hokkaido native horses were enumerated by their morphology and Gram staining, and then three major cellulolytic species were quantitated by recently developed competitive polymerase chain reaction (cPCR) assays. Fecal bacterial flora in horses showed drastic change between grazing on summer grassland pasture and grazing on winter woodland pasture mainly consisting of bamboo grass (Sasa nipponica). The number of total bacteria was decreased in winter samples, accompanied with a higher proportion of Gram negative rods and lower proportions of Gram negative cocci, Gram positive rods and cocci than those in summer. This high proportion of Gram negative rods was partly explained by the high cPCR-assay values for Fibrobacter succinogenes (a highly cellulolytic Gram negative rod) in winter samples. Of three major cellulolytic bacterial species, F. succinogenes was dominant in feces of Hokkaido native horses regardless of the sampling season. Feces of light horses mainly come from Thoroughbreds which had been kept with Hokkaido native horses, were taken in winter and employed for analysis. All three cellulolytic species were much less dominant in light horses. These results suggest that F. succinogenes contributes to fiber digestion in the hindgut of Hokkaido native horses, especially in winter woodland pasture where bamboo grass (Sasa nipponica) is mainly available.

MISC

• 子牛の腸管内における抗体の細菌への結合性

  大石睦, 鈴木裕, 三谷朋弘, 小池聡  日本畜産学会大会講演要旨  130th-  2022
• 子牛の成長に伴う腸管抗体産生能の変化

  廣田祥子, 林英明, 三谷朋弘, 芳賀聡, 小池聡, 小林泰男, 鈴木裕  日本畜産学会大会講演要旨  129th-  2021
• Development of salivary IgA secretory ability in weaned calves

  Hiroe Takahashi, Yutaka Suzuki, Satoshi Haga, Satoshi Koike, Yasuo Kobayashi  Advances in Animal Biosciences (Proceedings of the XIIIth International Symposium on Ruminant Physiology ISRP 2019)  10-  (3)  518 (P45)  2019/09  [Refereed][Not invited]
  
• The effect of chemerin as a host-derived factor on intestinal microbial activity in calves

  Yutaka Suzuki, Kanako Kubota, Hiroto Miura, Satoshi Haga, Sanggun Roh, Satoshi Koike, Yasuo Kobayashi  2018 ASAS-CSAS Annual Meeting ＆ Trade Show  135  2018/07  [Not refereed][Not invited]
  
• 黒毛和種牛ルーメン細菌叢の網羅的解析と重要細菌群の特定

  川西由希子, 橋本拓弥, 河内博貴, 遠藤哲代, 糟谷広高, 庄司則章, 小池聡, 小林泰男  日本畜産学会大会講演要旨  121st-  2016
• カシューナッツ殻液を給与したウシのルーメン真正細菌およびメタン細菌叢

  嵩千里, 宮澤のどか, 小池聡, 小林泰男, 真貝拓三, 三森真琴, 永西修, 長島協, 望月正巳  日本畜産学会大会講演要旨  115th-  2012
• カシューナッツ殻液給与がウシルーメン菌叢に及ぼす影響

  嵩千里, 真貝拓三, 三森真琴, 永西修, 長嶋協, 望月正己, 小池聡, 小林泰男  日本畜産学会大会講演要旨  112th-  2010
• カシューナッツ殻液28日間給与がマウス体重および血液成分に及ぼす影響

  小酒井貴晴, 遠藤翔子, 小笠原実咲, 癸生川彩, 香川菜美, 安部紗織, 伊藤茜, 佐藤侑美, 五十嵐美久, 小池聡, 小林泰男  日本栄養・食糧学会東北支部大会およびシンポジウム講演要旨集  44th-  2010
• Effects of Gluconic Acid and Methionine Hydroxy Analog on Growth and Intestinal Characteristics of Rats.

  H. Uchihori, S. Koike, Y. Kobayashi  MICROBIAL ECOLOGY  57-  (3)  581  -582  2009/04  [Not refereed][Not invited]
  
• Isolation and Partial Characterization of Prevotella Strains From Sheep Rumen.

  D. Matsui, S. Koike, Y. Kobayashi  MICROBIAL ECOLOGY  57-  (3)  575  -575  2009/04  [Not refereed][Not invited]
  
• Phylogenetic and phenotypic characterization of Fibrobacter succinogenes strains from the rumen

  Shinkai T, Matsumoto N, Koike S, Sawanon S, Kobayashi Y, Tanaka K  Biotechnology of Lignocellulose Degradation and Biomass Utilization  317  -320  2004  [Not refereed][Not invited]
  
• 乳牛新鮮糞におけるベロ毒素遺伝子の検出とその周年変化

  小林泰男, ELSAWY H, 小池聡, 中辻浩喜, 田中桂一  北海道畜産学会大会講演要旨  59th-  2003

Books etc

• ルーメンの科学

  板橋, 久雄, 小林, 泰男 (Contributor)
  農山漁村文化協会 2023/05 (ISBN: 9784540231209) 9,330p
• 新しい子牛の科学 : 胎生期から初産分娩まで

  家畜感染症学会 (Contributor子牛の第一胃発酵と腸内細菌叢)
  緑書房 2021/03 (ISBN: 9784895315876) 343p 152-156
• Antibiotic Resistance Genes in Natural Environments and Long-Term Effects

  (Contributor第8章)
  Nova Science Publishers (ISBN:978-1-53611-818-6) 2017/02
• 肉用牛の科学

  肉用牛研究会 (Contributor肉牛の第一胃内微生物群)
  養賢堂 2015/01 (ISBN: 4842505311) 398 104-106

Presentations

• ルーメン微生物の制御と反芻家畜生産のSDGs  [Invited]

  小池 聡

  第10回北海道畜産草地学会シンポジウム  2021/09
• 乳牛の常在微生物研究のルーツをたどる〜ルーメン微生物研究のアプローチと乳房炎研究への応用の可能性〜  [Invited]

  小池 聡

  第25回乳房炎研究会座談会  2020/10
• Effect of dietary condition on development of rumen microbiota in newborn calves (update)  [Invited]

  Satoshi Koike

  The 3rd International Symposium on Young Ruminant Rearing  2020/09
• Effect of dietary condition on development of rumen microbiota in newborn calves  [Invited]

  Satoshi Koike

  The 2nd International Symposium on Young Ruminant Rearing  2018/10

Association Memberships

• JAPANESE SOCIETY FOR ANIMAL NUTRITION AND METABOLISM   北海道畜産草地学会   日本微生物生態学会   日本応用糖質科学会   ルーメン研究会   日本畜産学会   

Research Projects

• 子牛の健全発育に資する消化管微生物の積極的な定着コントロールに関する研究

  日本学術振興会：科学研究費助成事業 基盤研究(B)

  Date (from‐to) : 2022/04 -2025/03 

  Author : 小池 聡
• Research on boosting mechanism of fiber digestion in key rumen bacterium by agricultural byproduct

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for JSPS Fellows

  Date (from‐to) : 2020/04 -2022/03 

  Author : 小池 聡, LAHRITA LUCY

   

  本研究ではF. succinogenesが保有する糖質分解酵素遺伝子（以下、GH遺伝子）のうち、機能がわかっている15個のGHに的を絞り、それらの遺伝子発現レベルを検討した。発現変動が見られたGH遺伝子は8つあり、2つは、マメ外皮添加によって発現量が減少した。これらの遺伝子は、GHファミリー8および9に属するエンドグルカナーゼであった。GHファミリー9に属する遺伝子は、結晶セルロースに対してほとんどまたはまったく活性を示さないが、可溶性セルロース誘導体およびさまざまな植物多糖類に対しては活性を示すことが知られている。植物の細胞壁のセルロースは結晶化した構造であるため、これらの遺伝子がコードする酵素はイナワラ消化への貢献度は低い可能性がある。マメ外皮添加によりイナワラ消化への貢献が低い酵素の遺伝子発現が低下するのであれば、酵素合成のコスト節約となり、結果としてF. succinogenesの効率的な繊維消化を促すかもしれない。 本研究で対象としたGH遺伝子のうち、エンドグルカナーゼ、キシラナーゼまたはセロデキストリンをコードする6つはマメ外皮の添加により発現量が向上した。これらのGH遺伝子の発現向上は、マメ外皮によるイナワラ消化のブースター効果を一部説明するものである。F. succinogenesは、植物細胞壁多糖類のセルロースとヘミセルロースの両方を分解する能力があることが知られている。多様なセルラーゼとヘミセルラーゼの発現向上は、複数の糖質分解酵素が複合的に作用することでF. succinogenesのセルロース分解が効率的に行われることを示唆している。 以上より、マメ外皮添加によりセルロース分解菌が保有するセルラーゼやキシラナーゼの遺伝子発現向上が認められ、本資材による繊維分解ブースト効果の機序を一部解明した。
• Methane mitigation from ruminants by wide range application of alkylpenol-containing plants

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)

  Date (from‐to) : 2018/04 -2022/03 

  Author : Kobayashi Yasuo

   

  Methane mitigation potential of alkylphenol-containing plants such as ginkgo fruit (GF) and cashew nut shell liquid (CL) was evaluated by the application as manure and/or feed additive. Considering local availability of each material, GF was supposed to use for Japanese cattle, while CL was for native cattle and swamp buffaloes in Thailand. The evaluations were made by monitoring changes of fermentation products and microbiota in in vitro culture systems and also in feeding studies. Both materials decreased methane production potential by the direct addition to feces with significant alteration of fecal microbial community, based on the selective anti-microbial actions. CL was further evaluated by feeding studies using Thani animals and was found to decrease methane production not only from the rumen fluid but also from feces. This accompanied with apparent changes in fecal microbiota.
• Exploration of microbial marker for prediction of metabolic disorder in ruminants

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research Challenging Research (Exploratory)

  Date (from‐to) : 2017/06 -2019/03 

  Author : Koike Satoshi

   

  Rumen microbes play a pivotal role in cattle productivity. The aim of this study was to identify the microbe(s) showing positive correlation with host productivity as a biomarker for prediction of productivity. As the first step, buccal swab as a proxy of rumen digesta was validated. This alternative sample enable to avoid laborious and time consuming sample collection by using stomach tube. Then, buccal swab samples were collected from Japanese Black cattle and employed for microbial analyses. Population size of Prevotella spp. seemed to have a positive correlation with the body weight of Japanese Black cattle . Therefore, Prevollta spp. can be used as a biomarker for prediction of body weight gain in the future.
• 黒毛和種牛の安定生産を保障するルーメン発酵と微生物機能の特定

  日本学術振興会：科学研究費補助金（基盤C）

  Date (from‐to) : 2014 -2016 

  Author : 小池 聡
• 黒毛和牛のルーメン微生物相と産肉成績の関連探索

  日本学術振興会：科学研究費補助金若手研究（B）

  Date (from‐to) : 2012 -2013 

  Author : 小池 聡
• 低メタン産生牛の特定をめざしたルーメン菌叢プロファイリング指標の確立

  日本学術振興会：科学研究費補助金基盤研究（B）

  Date (from‐to) : 2011 -2013 

  Author : 小林泰男
• 遺伝子発現調節による和牛肉の不飽和度向上技術の開発

  農林水産省：新たな農林水産政策を推進する実用技術開発事業

  Date (from‐to) : 2008 -2012 

  Author : 庄司則章
• Identification of high risk bacterial strains in rumen acidosis for the prevention of metabolic disorder in ruminants

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2010 -2011 

  Author : KOIKE Satoshi

   

  The present research revealed that genotypically and physiologically heterogeneous strains of S. bovis were distributed in the rumen. The specific genotypes of S. bovis strains are predominant when the animal is fed a high-grain diet. In addition, the balance of lactate producer/utilizer was altered by high-grain diet. This bacterial community shift might result in lactate accumulation and lower pH.
• Development of innovative rumen modifier to reduce methane production

  Japan Society for the Promotion of Science：Grants-in-Aid for Scientific Research

  Date (from‐to) : 2008 -2010 

  Author : KOBAYASHI Yasuo, KOIKE Satoshi, ENISHI Osamu, TAKENAKA Akio

   

  Cashew nut shell liquid, a novel rumen modifier, was evaluated for its potential to reduce methane from ruminant animals and possible mechanisms involved in it. The shell liquid selectively inhibited growth of several species of rumen bacteria to lead a dramatic shift of rumen microbiota. This resulted in rumen fermentation changes with less methane and more propionate production but without adverse effects on feed digestion and animal health. The feeding of shell liquid allowed more than 20% reduction of methane that had not been realized by any other modifiers. Therefore, future application of the shell liquid is highly expected.
• 草食動物消化管内での繊維分解において真に重要な細菌群の特定

  日本学術振興会：科学研究費補助金若手スタートアップ

  Date (from‐to) : 2007/04 -2008/03 

  Author : 小池 聡

   

  本課題の平成19年度における達成目標は、1)標的グループのルーメン内での挙動モニタリング、2)各種草食動物消化管内における標的グループの分布量把握および3)未知菌の培養化の3点であった。 1および2点目については平成18年度の試験で繊維分解に深く関与する可能性を示したPrevotella属に着目し、rea1-time PCRによる定量を行った。その結果、本属はルーメン内で10〜20%程度の密度で存在することを確認した。さらに、ルーメン内繊維片上に15%程度の密度で付着することを突き止め、Prevotella属が繊維片上で量的にメジャーであることを明らかにした。 3点目についてはこれまでに確立されている古典的培養法を基礎として、易分解性繊維成分に富む天然植物を培養基質として用いることで新規細菌の分離培養に成功した。新規に分離した繊維分解性細菌3菌株および非繊維分解性細菌4菌株はこれまでDNA情報でのみ存在が確認されてきた未培養細菌と91〜99%の16S rDNA塩基配列相同性を示し、本研究ではじめて分離に成功した菌株であった。新規株の繊維分解酵素活性を測定したところ、いずれの株もキシラナーゼやアラビノフラノシダーゼと言ったヘミセルロース分解に関与する酵素を保有し、その活性は既知のキシラン分解菌Butyrivibrio fibrisolvensの活性よりも高かった。したがって、本研究で初めて分離した新規菌株はルーメン内においてヘミセルロース分解に関与するものと考えられた。また、新規の非繊維分解性菌株を繊維分解菌と2菌共培養すると繊維分解率が向上することを確認した。 以上の結果はルーメン内での繊維分解において既知の繊維分解菌以外にも重要な細菌が存在することを示すものであり、草食動物消化管内での繊維分解を最適化する上で必要不可欠な情報を得ることができたものと確信している。