References
Amato, K. R., Martinez-Mota, R., Righini, N., Raguet-Schofield, M.,
Corcione, F. P., Marini, E., . . . Leigh, S. R. (2016). Phylogenetic and
ecological factors impact the gut microbiota of two Neotropical primate
species. Oecologia, 180 (3), 717-733.
doi:10.1007/s00442-015-3507-z
Baniel, A., Amato, K. R., Beehner, J. C., Bergman, T. J., Mercer, A.,
Perlman, R. F., . . . Snyder-Mackler, N. (2021). Seasonal shifts in the
gut microbiome indicate plastic responses to diet in wild geladas.Microbiome, 9 (1), 26. doi:10.1186/s40168-020-00977-9
Barelli, C., Albanese, D., Donati, C., Pindo, M., Dallago, C., Rovero,
F., . . . De Filippo, C. (2015). Habitat fragmentation is associated to
gut microbiota diversity of an endangered primate: implications for
conservation. Sci Rep, 5 , 14862. doi:10.1038/srep14862
Basabose, A. K. (2002). Diet composition of chimpanzees inhabiting the
montane forest of Kahuzi, Democratic Republic of Congo. Am J
Primatol, 58 , 1-21. doi:10.1002/ajp.10049
Benjamin Buchfink, C. X., Daniel H Huson (2015). Fast and sensitive
protein alignment using DIAMOND. Nat Methods, 12 , 59-60.
doi:10.1038/nmeth.3176
Bennett, G., Malone, M., Sauther, M. L., Cuozzo, F. P., White, B.,
Nelson, K. E., . . . Amato, K. R. (2016). Host age, social group, and
habitat type influence the gut microbiota of wild ring-tailed lemurs
(Lemur catta). Am J Primatol, 78 (8), 883-892.
doi:10.1002/ajp.22555
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible
trimmer for Illumina sequence data. Bioinformatics, 30 (15),
2114-2120. doi:10.1093/bioinformatics/btu170
Canfora, E. E., Meex, R. C. R., Venema, K., & Blaak, E. E. (2019). Gut
microbial metabolites in obesity, NAFLD and T2DM. Nat Rev
Endocrinol, 15 (5), 261-273. doi:10.1038/s41574-019-0156-z
Chivers, D. (1994). Functional anatomy of the gastrointestinal
tract. : Cambridge University Press.
Chivers, D. J., Hladik, C.M. (1980). Morphology of the gastrointestinal
tract in primates: comparisons with other mammals in relation to diet.J. Morphol, 166 , 337-386.
Christiane Liers, R. U., Harald Kellner, Do Huu Chi, Dang Thu Quynh,
Nguyen Dinh Luyen, Le Mai Huong, Martin Hofrichter, Do Huu Nghi. (2021).
Bioconversion of Lignocellulosic Materials with the Contribution of a
Multifunctional GH78 Glycoside Hydrolase from Xylaria polymorpha to
Release Aromatic Fragments and Carbohydrates. J Microbiol
Biotechnol, 31 (10), 1438-1445. doi:10.4014/jmb.2106.06053
Clayton, J. B., Gomez, A., Amato, K., Knights, D., Travis, D. A.,
Blekhman, R., . . . Johnson, T. J. (2018). The gut microbiome of
nonhuman primates: Lessons in ecology and evolution. Am J
Primatol, 80 (6), e22867. doi:10.1002/ajp.22867
Clayton, J. B., Vangay, P., Huang, H., Ward, T., Hillmann, B. M.,
Al-Ghalith, G. A., . . . Knights, D. (2016). Captivity humanizes the
primate microbiome. Proc Natl Acad Sci U S A, 113 (37),
10376-10381. doi:10.1073/pnas.1521835113
D., C. (1998). Primate digestion: Interactions among anatomy,
physiology, and feeding ecology. Evolutionary Anthropology, 7 (1),
8-20.
Degnan, P. H., Pusey, A. E., Lonsdorf, E. V., Goodall, J., Wroblewski,
E. E., Wilson, M. L., . . . Ochman, H. (2012). Factors associated with
the diversification of the gut microbial communities within chimpanzees
from Gombe National Park. Proc Natl Acad Sci U S A, 109 (32),
13034-13039. doi:10.1073/pnas.1110994109
Dinghua Li , C.-M. L., Ruibang Luo, Kunihiko Sadakane, Tak-Wah Lam.
(2015). MEGAHIT: An ultra-fast single-node solution for large and
complex metagenomics assembly via succinct de Bruijn graph.Bioinformatics, 31 , 1674–1676. doi:10.1093/bioinformatics/btv033
Dixon, P. (2003). VEGAN, a package of R functions for community ecologyJournal of Vegetation Science, 14 , 927-930.
doi:doi.org/10.1111/j.1654-1103.2003.
Emmanouil Angelakis, M. Y., Dipankar Bachar, Esam I Azhar,
Jean-Christophe Lagier, Fehmida Bibi, Asif A Jiman-Fatani, Maha Alawi,
Marwan A Bakarman, Catherine Robert, Didier Raoult. (2016). Gut
microbiome and dietary patterns in different Saudi populations and
monkeys. Sci Rep., 6 . doi:10.1038/srep32191
Fu Limin, N. B., Zhu Zhengwei, Wu Sitao, Li Weizhong,. (2012). CD-HIT:
accelerated for clustering the next-generation sequencing data.Bioinformatics, 28 (23), 3150-3152.
doi:10.1093/bioinformatics/bts565
Ganzhorn, J. U. (1992). Leaf chemistry andthe biomass of folivorous
primatesin tropical forests. Oecologia, 91 , 540-547.
Goldberg, T. L. (2008). Forest Fragmentation as Cause of Bacterial
Transmission among Nonhuman Primates, Humans, and Livestock, Uganda.Emerging Infectious Diseases, 14 (9), 1375-1382.
doi:10.3201/eid1409.071196
Hale, V. L., Tan, C. L., Niu, K., Yang, Y., Knight, R., Zhang, Q., . . .
Amato, K. R. (2018). Diet Versus Phylogeny: a Comparison of Gut
Microbiota in Captive Colobine Monkey Species. Microb Ecol,
75 (2), 515-527. doi:10.1007/s00248-017-1041-8
Hale, V. L., Tan, C.L., Niu, K., Yang, Y., Zhang, Q., Knight, R. (2019).
Gut microbiota in wild and captive Guizhou snub-nosed monkeys,
Rhinopithecus brelichi. Am J Primatol . doi:10.1002/ajp.22989
Hui Zhu, D. Z., Qiang Wang, Ning Wang, Bo Zeng, Lili Niu, Xueqin Ni.
(2018). Diarrhea-Associated Intestinal Microbiota in Captive Sichuan
Golden Snub-Nosed Monkeys (Rhinopithecus roxellana). Microbes
Environ, 29 , 249-256. doi:10.1264/jsme2.ME17163
Jianan Sang , D. Z., Tao Zhang, Qunfu Wu, Jiangkun Yu, Zhigang Zhang.
(2022). Convergent and Divergent Age Patterning of Gut Microbiota
Diversity in Humans and Nonhuman Primates. mSystems, 30 .
doi:10.1128/msystems.01512-21
Karasov, W. H., & Douglas, A. E. (2013). Comparative digestive
physiology. Compr Physiol, 3 (2), 741-783.
doi:10.1002/cphy.c110054
Kozak, M. (1983). Comparison of initiation of protein synthesis in
procaryotes, eucaryotes, and organelles. Microbiol Rev, 47 , 1-45.
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with
Bowtie 2. Nat Methods, 9 (4), 357-359. doi:10.1038/nmeth.1923
Lee, S., Cantarel, B., Henrissat, B., Gevers, D., Birren, B. W.,
Huttenhower, C., & Ko, G. (2014). Gene-targeted metagenomic analysis of
glucan-branching enzyme gene profiles among human and animal fecal
microbiota. ISME J, 8 (3), 493-503. doi:10.1038/ismej.2013.167
Ley, R. E. (2016). Gut microbiota in 2015: Prevotella in the gut: choose
carefully. Nat Rev Gastroenterol Hepatol, 13 (2), 69-70.
doi:10.1038/nrgastro.2016.4
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R.,
Bircher, J. S., . . . Gordon, J. I. (2008). Evolution of mammals and
their gut microbes. Science, 320 (5883), 1647-1651.
doi:10.1126/science.1155725
Li BG, P. R., Oxnard CE. (2002). Extinction of snub-nosed monkeys in
China during the past 400 years. Int J Primatol, 23 (6),
1227-1244.
Li, H., Qu, J., Li, T., Wirth, S., Zhang, Y., Zhao, X., & Li, X.
(2018). Diet simplification selects for high gut microbial diversity and
strong fermenting ability in high-altitude pikas. Appl Microbiol
Biotechnol, 102 (15), 6739-6751. doi:10.1007/s00253-018-9097-z
Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., . . . Meta,
H. I. T. C. (2014). An integrated catalog of reference genes in the
human gut microbiome. Nat Biotechnol, 32 (8), 834-841.
doi:10.1038/nbt.2942
Li, J., Zhong, H., Ramayo-Caldas, Y., Terrapon, N., Lombard, V.,
Potocki-Veronese, G., . . . Morgavi, D. P. (2020). A catalog of
microbial genes from the bovine rumen unveils a specialized and diverse
biomass-degrading environment. Gigascience, 9 (6).
doi:10.1093/gigascience/giaa057
Li, X., Liang, S., Xia, Z., Qu, J., Liu, H., Liu, C., . . . Xiao, L.
(2018). Establishment of a Macaca fascicularis gut microbiome gene
catalog and comparison with the human, pig, and mouse gut microbiomes.Gigascience, 7 (9). doi:10.1093/gigascience/giy100
Li, X., Wang, X., Wang, Z., Zhang, M., Wang, S., Xiang, Z., . . . Li, M.
(2022). The Relationship Between Gut Microbiome and Bile Acids in
Primates With Diverse Diets. Front Microbiol, 13 , 899102.
doi:10.3389/fmicb.2022.899102
Liu, R., Amato, K., Hou, R., Gomez, A., Dunn, D. W., Zhang, J., . . .
Guo, S. (2022). Specialized digestive adaptations within the hindgut of
a colobine monkey. Innovation (Camb), 3 (2), 100207.
doi:10.1016/j.xinn.2022.100207
Long YC, K. R., Zhong T, Xiao L. (1994). Report on the distribution,
population, and ecology of the Yunnan snub-nosed monkey (Rhinopithecus
bieti). Primates, 35 , 241-250.
Menzel, P., Ng, K. L., & Krogh, A. (2016). Fast and sensitive taxonomic
classification for metagenomics with Kaiju. Nat Commun, 7 , 11257.
doi:10.1038/ncomms11257
Mingpu Qi, Q. W., Shengtao Tong, Gang Zhao, Changmin Hu, Yingyu Chen,
Xiang Li, Wanji Yang , Yuchen Zhao, Sara Platto, Robertson Ian Duncan,
Jianguo Chen, Huanchun Chen, Aizhen Guo. (2017). Identification of
Atypical Enteropathogenic Escherichia coli O98 from Golden Snub-Nosed
Monkeys with Diarrhea in China. Front Vet Sci, 4 .
doi:10.3389/fvets.2017.00217
Naofumi Yoshida, T. Y., Tatsunori Osone, Tetsuya Hosooka, Masakazu
Shinohara, Seiichi Kitahama, Kengo Sasaki , Daisuke Sasaki, Takeshi
Yoneshiro, Tomohiro Suzuki, Takuo Emoto, Yoshihiro Saito, Genki Ozawa,
Yushi Hirota, Ken-Ichi Hirata. (2021). Bacteroides spp. promotes
branched-chain amino acid catabolism in brown fat and inhibits obesity.iScience, 24 (11), 103342. doi:10.1016/j.isci.2021.103342
Newman, T. M., Shively, C. A., Register, T. C., Appt, S. E., Yadav, H.,
Colwell, R. R., . . . Cook, K. L. (2021). Diet, obesity, and the gut
microbiome as determinants modulating metabolic outcomes in a non-human
primate model. Microbiome, 9 (1), 100.
doi:10.1186/s40168-021-01069-y
P., L. (1988). The mammalian herbivore stomach. Stuttgart/New
York: Gustav Fischer Verlag .
Palevich, N., Kelly, W. J., Leahy, S. C., Denman, S., Altermann, E.,
Rakonjac, J., & Attwood, G. T. (2019). Comparative Genomics of Rumen
Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading
Capabilities. Appl Environ Microbiol, 86 (1).
doi:10.1128/AEM.01993-19
Pattabiraman, S., & Warnow, T. (2021). Profile Hidden Markov Models Are
Not Identifiable. IEEE/ACM Trans Comput Biol Bioinform, 18 (1),
162-172. doi:10.1109/TCBB.2019.2933821
Petia Kovatcheva-Datchary, A. N., Rozita Akrami, Ying Shiuan Lee, Filipe
De Vadder, Tulika Arora, Anna Hallen, Eric Martens, Inger Björck,
Fredrik Bäckhed (2015). Dietary Fiber-Induced Improvement in Glucose
Metabolism Is Associated with Increased Abundance of Prevotella.Cell Metab, 22 (6), 971-982. doi:10.1016/j.cmet.2015.10.001
Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C.,
. . . Wang, J. (2010). A human gut microbial gene catalogue established
by metagenomic sequencing. Nature, 464 (7285), 59-65.
doi:10.1038/nature08821
Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., . . . Wang, J.
(2012). A metagenome-wide association study of gut microbiota in type 2
diabetes. Nature, 490 (7418), 55-60. doi:10.1038/nature11450
Quan Gouqiang, X. J. (2002). Research on the golden monkey :
Beijing:Science and Education Publishing House.
Ransom-Jones, E., Jones, D. L., McCarthy, A. J., & McDonald, J. E.
(2012). The Fibrobacteres: an important phylum of cellulose-degrading
bacteria. Microb Ecol, 63 (2), 267-281.
doi:10.1007/s00248-011-9998-1
Sylwia Smolinska, L. O. M. (2016). Microbiome-Host Immune System
Interactions. Semin Liver Dis, 36 , 317-326.
doi:10.1055/s-0036-1593883
Tayte P Campbell, X. S., Vishal H Patel, Crickette Sanz, David Morgan,
Gautam Dantas. (2020). The microbiome and resistome of chimpanzees,
gorillas, and humans across host lifestyle and geography. ISME J.,
16 (6), 1584-1599. doi:10.1038/s41396-020-0634-2
Thingholm, L. B., Ruhlemann, M. C., Koch, M., Fuqua, B., Laucke, G.,
Boehm, R., . . . Huttenhower, C. (2019). Obese Individuals with and
without Type 2 Diabetes Show Different Gut Microbial Functional Capacity
and Composition. Cell Host Microbe, 26 (2), 252-264 e210.
doi:10.1016/j.chom.2019.07.004
Trevelline, B. K., & Moeller, A. H. (2022). Robustness of Mammalian Gut
Microbiota to Humanization in Captivity. Front Ecol Evol, 9 .
doi:10.3389/fevo.2021.785089
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E.
R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with
increased capacity for energy harvest. Nature, 444 (7122),
1027-1031. doi:10.1038/nature05414
Wang, X., Wang, Z., Pan, H., Qi, J., Li, D., Zhang, L., . . . Li, M.
(2021). Captivity Influences the Gut Microbiome of Rhinopithecus
roxellana. Front Microbiol, 12 , 763022.
doi:10.3389/fmicb.2021.763022
Wenhan Zhu, A. L., Mark Borodovsky. (2010). Ab Initio Gene
Identification in Metagenomic Sequences. Nucleic Acids Res, 38 .
doi:10.1093/nar/gkq27
Xia, W., Zhao, M., Wang, D., Wang, F., Chen, H., Liu, G., . . . Li, D.
(2022). Invasion and defense of the basic social unit in a nonhuman
primate society leads to sexual differences in the gut microbiome.Integr Zool, 17 (1), 168-180. doi:10.1111/1749-4877.12608
Xiao, L., Estellé, J., Kiilerich, P., Ramayo-Caldas, Y., Xia, Z., Feng,
Q., . . . Wang, J. (2016). A reference gene catalogue of the pig gut
microbiome. Nature Microbiology, 1 (12).
doi:10.1038/nmicrobiol.2016.161
Xiao, L., Feng, Q., Liang, S., Sonne, S. B., Xia, Z., Qiu, X., . . .
Kristiansen, K. (2015). A catalog of the mouse gut metagenome.Nature Biotechnology, 33 (10), 1103-1108. doi:10.1038/nbt.3353
Xie, F., Jin, W., Si, H., Yuan, Y., Tao, Y., Liu, J., . . . Mao, S.
(2021). An integrated gene catalog and over 10,000 metagenome-assembled
genomes from the gastrointestinal microbiome of ruminants.Microbiome, 9 (1), 137. doi:10.1186/s40168-021-01078-x
Xu, B., Xu, W., Li, J., Dai, L., Xiong, C., Tang, X., . . . Huang, Z.
(2015). Metagenomic analysis of the Rhinopithecus bieti fecal microbiome
reveals a broad diversity of bacterial and glycoside hydrolase profiles
related to lignocellulose degradation. BMC Genomics, 16 , 174.
doi:10.1186/s12864-015-1378-7
Yang Gu , Y. D., Cong Ren, Zhe Sun, Dmitry A Rodionov, Weiwen Zhang,
Sheng Yang, Chen Yang and, & Jiang, W. (2010). Reconstruction of xylose
utilization pathway and regulons in Firmicutes. BMC Genomics .
doi:10.1186/1471-2164-11-255
Yao, L., Li, X., Zhou, Z., Shi, D., Li, Z., Li, S., . . . Xiao, Y.
(2021). Age-Based Variations in the Gut Microbiome of the Shennongjia
(Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis).Biomed Res Int, 2021 , 6667715. doi:10.1155/2021/6667715
Yoav Benjamini, Y. H. (1995). Controlling the False Discovery Rate: a
Practical and Powerful Approach to Multiple Testing. Wiley for the
Royal Statistical Society, 57 . doi:10.1111/j.2517-6161.1995.tb02031.x
Zhang, X., Chen, B. D., Zhao, L. D., & Li, H. (2020). The Gut
Microbiota: Emerging Evidence in Autoimmune Diseases. Trends Mol
Med, 26 (9), 862-873. doi:10.1016/j.molmed.2020.04.001
Zhang, Z., Xu, D., Wang, L., Hao, J., Wang, J., Zhou, X., . . . Shi, P.
(2016). Convergent Evolution of Rumen Microbiomes in High-Altitude
Mammals. Curr Biol, 26 (14), 1873-1879.
doi:10.1016/j.cub.2016.05.012
Zhou, X., Wang, B., Pan, Q., Zhang, J., Kumar, S., Sun, X., . . . Li, M.
(2014). Whole-genome sequencing of the snub-nosed monkey provides
insights into folivory and evolutionary history. Nat Genet,
46 (12), 1303-1310. doi:10.1038/ng.3137
Zhu, J., Ren, H., Zhong, H., Li, X., Zou, Y., Han, M., . . . Xiao, L.
(2020). An expanded gene catalog of the mouse gut metagenome.
doi:10.1101/2020.09.16.299339