2019年03月, 日本畜産学会, Animal Science Journalレビュアー賞　　　　　　　　　　　　　　　

2017年01月, AJAS 2016 ベストレビュアー賞　　　　　　　　　　　　　　　
KOIKE Satoshi

2015年03月, 日本畜産学会, Animal Science Journalレビュアー賞　　　　　　　　　　　　　　　

2011年, 日本畜産学会優秀論文賞　　　　　　　　　　　　　　　
日本国

2007年, 日本畜産学会奨励賞　　　　　　　　　　　　　　　
日本国

Coconut Fatty Acid Distillate Ca-Soap with Different Calcium Sources: Effects of Varied Proportions of Protected and Unprotected Fat Supplementation in Dairy Rations
Rika Zahera, Mega Indah Pratiwi, Ainissya Fitri, Satoshi Koike, Idat Galih Permana, Despal
Dairy, 2024年09月13日
英語, 研究論文（学術雑誌）, This study aimed to compare calcium oxide (CaO) and calcium chloride (CaCl2) as calcium sources for coconut fatty acid distillate (CFAD) calcium soap (Ca-soap) production and to evaluate the supplementation ratios of unprotected and protected CFAD in dairy rations to optimize rumen function. This research included two steps: (1) assessing the protection strength of Ca-soap made with CaO and CaCl2 at mole ratios of Ca to CFAD of 1, 1.5, 2, and 2.5; (2) evaluating CFAD supplementation in an in vitro dairy ration study using a 5 × 4 randomized factorial block design. Factor A compared unprotected and protected CFAD ratios of A1 = 100:0, A2 = 75:25, A3 = 50:50, A4 = 25:75, and A5 = 0:100, and factor B compared supplementation levels of B1 = 0%, B2 = 1%, B3 = 2%, and B4 = 3%. CaCl2 at a 2.5-mole ratio to CFAD produced the lowest acid value and the carboxylic acid (C=O) chemical bond. Complete protection (0:100) exhibited the highest densities of Bacteroides and nutrient digestibility (p < 0.05) without significantly affecting rumen fermentability (p > 0.05). Higher CFAD levels significantly reduced methanogens and protozoa (p < 0.05) without significantly affecting estimated methane production. In conclusion, CaCl2 at a 2.5-mole ratio to CFAD provided the best protection, and its complete protection in CFAD supplementation optimized rumen function.

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年01月
研究論文（学術雑誌）

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, Springer Science and Business Media LLC, 2023年07月14日
研究論文（学術雑誌）

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年05月12日
研究論文（学術雑誌）

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年01月
研究論文（学術雑誌）

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, Springer Science and Business Media LLC, 2022年06月, ［査読有り］, ［最終著者, 責任著者］
英語, 研究論文（学術雑誌）, 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, Frontiers Media SA, 2022年03月24日, ［査読有り］, ［最終著者, 責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）, 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., 12776927

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, Wiley, 2022年01月
研究論文（学術雑誌）

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, American Dairy Science Association, 2021年10月, ［査読有り］, ［筆頭著者, 責任著者］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, American Dairy Science Association, 2021年09月, ［査読有り］, ［最終著者, 責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Wiley, 2021年08月18日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）, 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, 2021年08月17日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2021年08月05日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2021年07月27日, ［査読有り］, ［最終著者, 責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Wiley, 2021年07月26日, ［査読有り］, ［筆頭著者, 責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）, 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年05月30日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）, 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, 2021年05月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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年01月16日, ［査読有り］, ［最終著者, 責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）, 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., 10810054

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年01月04日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, 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年10月05日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, 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年09月29日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）, 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, Wiley, 2020年04月03日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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年11月14日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）, 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, Springer Science and Business Media LLC, 2019年06月26日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Elsevier BV, 2019年06月15日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Wiley, 2019年04月14日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, 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, Asian Australasian Association of Animal Production Societies, 2019年02月14日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）, 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, Wageningen Academic Publishers, 2018年12月07日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, 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, American Dairy Science Association, 2018年12月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Wiley, 2018年09月05日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Nature Publishing Group, 2018年03月19日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Wiley, 2018年02月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Springer Science and Business Media LLC, 2017年11月24日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, 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, 2017年11月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2017年11月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2017年11月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 61, 2, 33‐41, 41, 家畜栄養生理研究会, 2017年09月, ［査読有り］, ［招待有り］, ［国内誌］
英語

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, 61, 2, 13‐19, 19, 家畜栄養生理研究会, 2017年09月, ［査読有り］, ［招待有り］, ［国内誌］
英語

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, 2017年08月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2017年03月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2017年02月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2016年12月, ［査読有り］, ［招待有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2015年11月26日, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

Monitoring of gene expression in Fibrobacter succinogenes S85 under the co-culture with non-fibrolytic ruminal bacteria
Fukuma Naoki M., Koike Satoshi, Kobayashi Yasuo
Archives of Microbiology, 197, 2, 269, 276, 2015年03月, ［査読有り］, ［責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2014年05月, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2014年03月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2013年08月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2012年11月, ［査読有り］, ［責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2012年10月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2012年01月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

Agricultural by-products as modulators of rumen microbiota　　　　　　　　　　　　　　　
Kobayashi Y, Shinkai T, Koike S
International Colloquium on Rumen Microbiology, 49, 60, 2012年, ［査読有り］, ［招待有り］, ［国際誌］

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, 2011年12月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

Effect of liquid whey feeding on fecal microbiota of mature and growing pigs
KOBAYASHI Yasuo, ITOH Aya, MIYAWAKI Kanae, KOIKE Satoshi, IWABUCHI Osamu, IIMURA Yuji, KOBASHI Yuri, KAWASHIMA Tomoyuki, WAKAMATSU Junichi, HATTORI Akihito, MURAKAMI Hiroshi, MORIMATSU Fumiki, NAKAEBISU Takashi, HISHINUMA Takeshi
Animal science journal, 82, 4, 607, 615, 2011年08月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 316, 1, 51, 60, 2011年03月, ［査読有り］, ［責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2010年11月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2010年04月, ［査読有り］, ［筆頭著者］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

Molecular Monitoring and Isolation of Previously Uncultured Bacterial Strains from the Sheep Rumen
Koike S., Handa Y., Goto H., Sakai K., Miyagawa E., Matsui H., Ito S., Kobayashi Y.
Applied and Environmental Microbiology, 76, 6, 1887, 1894, 2010年03月15日, ［査読有り］, ［筆頭著者, 責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）

Genetic diversity and diet specificity of ruminal Prevotella revealed by 16S rRNA gene-based analysis
Bekele Aschalew Z., Koike Satoshi, Kobayashi Yasuo
FEMS Microbiology Letters, 305, 1, 49, 57, 2010年03月04日, ［査読有り］, ［責任著者］, ［国際誌］
英語, 研究論文（学術雑誌）

Molecular Analyses of an Unusual Translesion DNA Polymerase from Methanosarcina acetivorans C2A
Lin Li-Jung, Yoshinaga Aya, Lin Yuyen, Guzman Claudia, Chen Yi-Hsing, Mei Shou, Lagunas Angelica M., Koike Satoshi, Iwai Shigenori, Spies M. Ashley, Nair Satish K., Mackie Roderick I., Ishino Yoshizumi, Cann Isaac K.O.
Journal of Molecular Biology, 397, 1, 13, 30, 2010年03月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Wiley, 2009年05月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

Fibrolytic Rumen Bacteria: Their Ecology and Functions
Satoshi Koike, Yasuo Kobayashi
ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES, 22, 1, 131, 138, 2009年01月, ［招待有り］, ［筆頭著者］, ［国際誌］
英語

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, Springer Science and Business Media LLC, 2008年05月, ［査読有り］, ［招待有り］, ［国際誌］
英語, 研究論文（学術雑誌）

Phylogenetic analysis of hindgut microbiota in Hokkaido native horses compared to light horses
YAMANO Hidehisa, KOIKE Satoshi, KOBAYASHI Yasuo, HATA Hiroshi
Animal science journal, 79, 2, 234, 242, 2008年04月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2007年08月, ［査読有り］, ［筆頭著者］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

Validation and application of real-time polymerase chain reaction assays for representative rumen bacteria
KOIKE Satoshi, YABUKI Hiroyoshi, KOBAYASHI Yasuo
Animal science journal, 78, 2, 135, 141, 2007年04月, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2006年12月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

Hindgut microbes, fermentation and their seasonal variations in Hokkaido native horses compared to light horses
Kobayashi Yasuo, Koike Satoshi, Miyaji Makoto, HATA Hiroshi, TANAKA Keiichi
Ecological research, 21, 2, 285, 291, 2006年03月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

Ruminal distribution of the cellulolytic bacterium Fibrobacter succinogenes in relation to its phylogenetic grouping
KOIKE Satoshi, PAN Jun, SUZUKI Tomoyuki, TAKANO Toru, OSHIMA Chihiro, KOBAYASHI Yasuo, TANAKA Keiichi
Animal science journal, 75, 5, 417, 422, Wiley, 2004年10月, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2004年09月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, 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
TAGUCHI Hidenori, KOIKE Satoshi, KOBAYASHI Yasuo, CANN Isaac K. O., KARITA Shuichi
Animal science journal, 75, 4, 325, 332, Wiley, 2004年08月, ［査読有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

Rumen microbes and fermentation of wild sika deer on the Shiretoko peninsula of Hokkaido Island, Japan
Ichimura Yasuhiro, Yamano Hidehisa, Takano Toru, KOIKE Satoshi, KOBAYASHI Yasuo, TANAKA Keiichi, OZAKI Nobuo, SUZUKI Masatsugu, OKADA Hideaki, YAMANAKA Masami
Ecological research, 19, 4, 389, 395, 2004年07月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2004年07月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, Asian Australasian Association of Animal Production Societies, 2004年06月01日, ［査読有り］, ［招待有り］, ［国際共著］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2004年02月, ［招待有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2004年01月01日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2003年12月, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）

Expression and export of a Ruminococcus albus cellulase in Butyrivibrio fibrisolvens through the use of an alternative gene promoter and signal sequence
Yasuo Kobayashi;Hidenori Taguchi;Takashi N Goto;Satoshi Koike;Kunio Ohmiya
Can. J. Microbiol., 49, 6, 375, 382, 2003年06月01日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2003年04月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

Kinetics of in sacco fiber-attachment of representative ruminal cellulolytic bacteria monitored by competitive PCR
KOIKE S
Journal of Dairy Science, 86, 4, 1429, 1435, 2003年04月, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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, 2003年02月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）

Development and use of competitive PCR assays for the rumen cellulolytic bacteria : Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens
KOIKE S.
FEMS Microbiology Letters, 204, 2, 361, 366, 2001年11月, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）

Fecal Bacteria in Hokkaido Native Horses as Characterized by Microscopic Enumeration and Competitive Polymerase Chain Reaction Assays.
KOIKE Satoshi, SHINGU Yuko, INABA Hiroyuki, KAWAI Masahito, KOBAYASHI Yasuo, HATA Hiroshi, TANAKA Keiichi, OKUBO Masahiko
Journal of Equine Science, 11, 2, 45, 50, Japanese Society of Equine Science, 2000年, ［査読有り］, ［筆頭著者］, ［国際誌］
英語, 研究論文（学術雑誌）

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年

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年

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年09月, ［査読有り］
英語, 研究発表ペーパー・要旨（国際会議）

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年07月
英語, 研究発表ペーパー・要旨（国際会議）

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年

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年

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年

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年

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年04月
英語, 研究発表ペーパー・要旨（国際会議）

Isolation and Partial Characterization of Prevotella Strains From Sheep Rumen.
D. Matsui, S. Koike, Y. Kobayashi, MICROBIAL ECOLOGY, 57, 3, 575, 575, 2009年04月
英語, 研究発表ペーパー・要旨（国際会議）

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年

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年

ルーメンの科学
板橋, 久雄, 小林, 泰男
農山漁村文化協会, 2023年05月, 9784540231209, 9,330p, 日本語, ［分担執筆］

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, 子牛の第一胃発酵と腸内細菌叢
緑書房, 2021年03月, 9784895315876, 343p, 152-156, 日本語, ［分担執筆］

Antibiotic Resistance Genes in Natural Environments and Long-Term Effects　　　　　　　　　　　　　　　
第8章
Nova Science Publishers (ISBN:978-1-53611-818-6), 2017年02月, ［国際共著］, ［分担執筆］

肉用牛の科学
肉用牛研究会, 肉牛の第一胃内微生物群
養賢堂, 2015年01月09日, 4842505311, 398, 104-106, 日本語, 学術書, ［分担執筆］

ルーメン微生物の制御と反芻家畜生産のSDGs　　　　　　　　　　　　　　　
小池 聡
第10回北海道畜産草地学会シンポジウム, 2021年09月11日, 日本語, シンポジウム・ワークショップパネル（指名）
［招待講演］, ［国内会議］

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〜　　　　　　　　　　　　　　　
小池 聡
第25回乳房炎研究会座談会, 2020年10月24日, 日本語, シンポジウム・ワークショップパネル（指名）
［招待講演］, ［国内会議］

Effect of dietary condition on development of rumen microbiota in newborn calves (update)　　　　　　　　　　　　　　　
Satoshi Koike
The 3rd International Symposium on Young Ruminant Rearing, 2020年09月28日, 英語, シンポジウム・ワークショップパネル（指名）
［招待講演］, ［国際会議］

Effect of dietary condition on development of rumen microbiota in newborn calves　　　　　　　　　　　　　　　
Satoshi Koike
The 2nd International Symposium on Young Ruminant Rearing, 2018年10月22日, 英語, シンポジウム・ワークショップパネル（指名）
［招待講演］, ［国際会議］

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
科学研究費助成事業
2022年04月01日 - 2025年03月31日
小池 聡
本研究では自発的な固形飼料摂取が始まる前に粗飼料の早期経口投与を実施し、子牛消化管微生物の積極的な定着コントロールの可能性を探った。
前年度に開始した新生子牛を対象とした試験では、哺乳期における粗飼料の早期経口投与の有益な効果、すなわち生後21日までの増体の向上ならびに消化管（ルーメンおよび腸内）での有用菌の増加が確認された。
本年度は試験対象牛を同一農場にて同一の飼料条件で継続飼養し、哺乳期の飼養管理の違いがその後の生産性に及ぼす影響の追跡調査に着手した。これまでのところ、9ヶ月齢時点での体重や飼料摂取量には試験区間で違いが見られなかった。ルーメン内容物の解析を実施したところ、VFA産生量と組成ならびに菌叢構成にも明確な違いは認められなかった。したがって、哺乳期における粗飼料の早期経口投与は、育成期における発育ならびにルーメン発酵に影響を及ぼさないことが確認された。
前年度の試験において、粗飼料の早期経口投与により、腸内（糞便中）のLactobacillus属細菌が増加することを確認した。本年度はロングリードシーケンサーを用いて、Lactobacillus属細菌の種レベルでの特定を試みた。16S rRNA遺伝子解析より特定されたLactobacillus属細菌の約50％は未培養の細菌種であったが、残り50％はLactobaciilus reuteri、Lactobacillus gasseriおよびLactobacillus johnsoniiであった。これらの3種の乳酸菌はいずれもプロバイオティック効果を持つことが報告されている。したがって、粗飼料の早期経口投与により子牛の腸内では有用な乳酸菌が増殖することを確認した。
日本学術振興会, 基盤研究(B), 北海道大学, 23K23753

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
科学研究費助成事業 基盤研究(B)
2022年04月01日 - 2025年03月31日
小池 聡
日本学術振興会, 基盤研究(B), 北海道大学, 22H02488

農業副産物による重要ルーメン菌群の繊維分解活性向上とその作用機序に関する研究
科学研究費助成事業 特別研究員奨励費
2020年04月 - 2022年03月
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。
日本学術振興会, 特別研究員奨励費, 北海道大学, 競争的資金, 20F20102

機能性アルキルフェノール含有植物の多面的活用による反すう家畜由来メタンガスの削減
科学研究費助成事業 基盤研究(B)
2018年04月 - 2022年03月
小林 泰男
温室効果ガスであるメタンは、反芻家畜ルーメン発酵産物のひとつとして生成される一方で、排泄物からも生じる。よってこれらの堆積や放置が想定される場合は低減が必要である。ギンナン果肉は抗菌性フェノール成分（アルキルフェノール）を含有しているため、牛排泄物に混和した場合、それらの菌叢および発酵産物を変化させると考えられる。そこで、ギンナン果肉がウシ糞便およびスラリーの発酵におよぼす影響をメタンをはじめとした発酵産物や菌叢に焦点を当て評価した。
ホルスタイン種乳牛の新鮮糞便および貯留スラリーを容器に分け入れ、ギンナン果肉を添加した方をギンナン区，無添加の方を対照区とした。ギンナン区にはギンナン果肉を6.4％（糞便200 gに対しギンナン果肉12.8 g）加え混合した。これらの容器を30℃のインキュベーターに入れて0、30、60、90、180日間を放置し、各放置期間終了時に，糞便またはスラリーを緩衝液で希釈しハンゲートチューブに入れ、 30℃で168時間培養した。培養後は発酵産物（ガスと短鎖脂肪酸）および菌叢の分析を行った。
糞便のメタン生成量は30日以降180日まで全期間においてギンナン区で減少した。ギンナン果肉の添加によって全期間を通して酢酸モル比は低下し、プロピオン酸モル比は上昇した。スラリーのメタン生成量はギンナン果肉の添加により、0日から90日まで期間を通じて減少した。0日ではギンナン区において総短鎖脂肪酸、酢酸およびプロピオン酸濃度は増加したが、酢酸比は低下し、プロピオン酸比は上昇した。30日以降ギンナン区では短鎖脂肪酸（特に酢酸）の蓄積が確認された。PCR-DGGEによる菌叢解析から，ギンナン果肉の添加により糞便およびスラリー双方で真正細菌叢、メタン古細菌叢ともに変化したことが確認された。これらより、ギンナン果肉は牛排泄物からのメタン削減に有効なことが示唆された。
日本学術振興会, 基盤研究(B), 北海道大学, 研究分担者, 18H02322

反芻家畜の代謝性疾患を予見するためのバイオマーカー探索
科学研究費助成事業 挑戦的研究(萌芽)
2017年06月 - 2019年03月
小池 聡
ウシは第一胃（ルーメン）に共生する微生物に飼料の分解を委ねており、ルーメン微生物の働きは乳肉生産に大きく影響する。本研究では、ウシの生産性と関連するルーメン微生物を特定し、これをバイオマーカーとして利用する可能性について検討した。まず、ウシや作業者の負担を軽減するために、ルーメン内容物の代替として口腔内の反芻残渣が利用可能であることを確認し、サンプリング手法の簡便性を大きく改善した。この手法を応用して、黒毛和種肥育牛においてはPrevotella属細菌群の分布量と体重に正の相関がある可能性を明らかにした。今後、本属細菌を体重増加のバイオマーカーとして活用できるかもしれない。
日本学術振興会, 挑戦的研究(萌芽), 北海道大学, 研究代表者, 17K19315

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
科学研究費補助金（基盤C）
2014年 - 2016年
小池 聡
日本学術振興会, 研究代表者, 競争的資金

黒毛和牛のルーメン微生物相と産肉成績の関連探索
科学研究費補助金若手研究（B）
2012年 - 2013年
小池 聡
日本学術振興会, 研究代表者, 競争的資金

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
科学研究費補助金基盤研究（B）
2011年 - 2013年
小林泰男
日本学術振興会, 競争的資金

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　　　　　　　　　　　　　　　
新たな農林水産政策を推進する実用技術開発事業
2008年 - 2012年
庄司則章
農林水産省, 競争的資金

反すう家畜の代謝障害予防をめざしたアシドーシス誘発高リスク菌株の特定
科学研究費補助金若手研究（B）
2010年 - 2011年
小池 聡
本研究では、反芻動物第一胃(ルーメン)細菌・ストレプトコッカス・ボビスは遺伝的・生理的に多様であることを明らかにした。また、穀物飼料を多給すると特定のストレプトコッカス・ボビス菌株が優勢となること、またその他の乳酸産生菌/利用菌のバランスが変化することが判明した。この菌叢変化が乳酸の蓄積、pHの低下といったルーメン環境の悪化につながる可能性を示唆した。
日本学術振興会, 若手研究(B), 北海道大学, 研究代表者, 競争的資金, 22780238

メタンの革新的削減をめざしたルーメン発酵制御物質の開発
科学研究費補助金基盤研究（B）
2008年 - 2010年
小林泰男
新規メタン低減物質候補であるカシューナッツ殻油の反芻家畜への給与効果と作用機序について検討した。殻油はルーメン内の細菌の増殖を選択的に抑制することで菌叢が変化し、低メタン・高プロピオン酸生成型の発酵が導かれた。その結果、飼料消化や健康をがい阻害することなく、20%以上のメタン低減が可能となった。このように効果的な天然物質は初めてのもので今後の実用化が期待される。
日本学術振興会, 基盤研究(B), 北海道大学, 競争的資金, 20380146

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
科学研究費補助金若手スタートアップ
2007年04月 - 2008年03月
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。
日本学術振興会, 若手研究(スタートアップ), 北海道大学, 研究代表者, 競争的資金, 18880002