Nội dung được dịch bởi AI, chỉ mang tính chất tham khảo
Cải thiện tiêu chuẩn phân tích hệ vi sinh vật đường ruột từ mẫu phân: những hiểu biết từ sinh học thực địa của khỉ Macaca fuscata yakui trên đảo Yakushima
Tóm tắt
Phân tích gen ribosomal RNA 16S dựa trên DNA phân với sự hỗ trợ của các trình tự thế hệ mới cho phép chúng ta hiểu khả năng thích nghi của hệ vi sinh vật đường ruột ở động vật với các môi trường sống cụ thể của chúng. Các kỹ thuật truyền thống để phân tích hệ vi sinh vật phân đã được phát triển trong các bối cảnh rộng lớn hơn do sinh học con người định nghĩa; do đó, nhiều kỹ thuật này không thể áp dụng ngay lập tức cho các loài linh trưởng hoang dã không phải con người. Để xây dựng một quy trình thí nghiệm tiêu chuẩn cho phân tích hệ vi sinh vật đường ruột ở động vật hoang dã, chúng tôi đã chọn khỉ macaque Nhật Bản (Macaca fuscata yakui) trên đảo Yakushima. Chúng tôi đã thử nghiệm các quy trình khác nhau cho từng giai đoạn xử lý mẫu phân: lưu trữ, chiết xuất DNA và lựa chọn vùng trình tự trong gen 16S rRNA của vi khuẩn. Chúng tôi cũng phân tích hệ vi sinh vật đường ruột của khỉ macaque Nhật Bản nuôi nhốt làm nhóm đối chứng. So sánh các mẫu thu được từ những con khỉ macaque giống hệt nhau nhưng được xử lý bằng các quy trình khác nhau cho thấy rằng các phương pháp lưu trữ được thử nghiệm (RNAlater và dung dịch phân giải) cho ra thành phần các đơn vị phân loại hoạt động vi khuẩn (OTUs) tương tự như phương pháp lưu trữ đông lạnh tiêu chuẩn, mặc dù độ phong phú tương đối của mỗi OTU chịu ảnh hưởng về mặt định lượng. Phân loại các nhóm vi khuẩn được phát hiện cũng chịu ảnh hưởng đáng kể bởi vùng được giải trình tự, cho thấy rằng các vùng trình tự và các cặp primer chuỗi polymerase (PCR) tương ứng cho gen 16S rRNA cần được lựa chọn một cách cẩn thận. Nghiên cứu này cải thiện các phương pháp tiêu chuẩn hiện tại cho phân tích hệ vi sinh vật ở các loài linh trưởng hoang dã không phải con người. Khỉ macaque Nhật Bản đã được chứng minh là mô hình phù hợp để hiểu khả năng thích nghi của hệ vi sinh vật với các môi trường khác nhau.
Từ khóa
#hệ vi sinh vật #khỉ macaque Nhật Bản #phân tích DNA phân #mẫu phân #phương pháp tiêu chuẩnTài liệu tham khảo
Agetsuma N, Nakagawa N (1998) Effects of habitat differences on feeding behaviors of Japanese monkeys: comparison between Yakushima and Kinkazan. Primates 39:275–289
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
Amato KR, Yeoman CJ, Kent A, Righini N, Carbonero F et al (2013) Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J 7:1344–1353
Amato KR, Leigh SR, Kent A, Mackie RI, Yeoman CJ et al (2015) The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Microb Ecol 69:434–443
Amato KR, Metcalf JL, Song SJ, Hale VL, Clayton J et al (2016) Using the gut microbiota as a novel tool for examining colobine primate GI health. Glob Ecol Conserv 7:225–237
Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T et al (2011) Enterotypes of the human gut microbiome. Nature 473:174–180
Asquith PJ (1989) Provisioning and the study of free-ranging primates: history, effects, and prospects. Yearb Phys Anthropol 32:129–158
Bahl MI, Bergström A, Licht TR (2012) Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett 329:193–197
Balvočiūtė M, Huson DH (2017) SILVA, RDP, greengenes, NCBI and OTT—how do these taxonomies compare? BMC Genom 18(Suppl 2):114
Blekhman R, Tang K, Archie EA, Barreiro LB, Johnson ZP et al (2016) Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Sci Rep 6:31519
Camacho-Sanchez M, Burraco P, Gomez-Mestre I, Leonard JA (2013) Preservation of RNA and DNA from mammal samples under field conditions. Mol Ecol Resour 13:663–673
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336
Choo JM, Leong LE, Rogers GB (2015) Sample storage conditions significantly influence faecal microbiome profiles. Sci Rep 5:16350
Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM et al (2016) Captivity humanizes the primate microbiome. Proc Natl Acad Sci USA 113:10376–10381
Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A et al (2017) Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol 35:1069–1076
Flores R, Shi J, Yu G, Ma B, Ravel J et al (2015) Collection media and delayed freezing effects on microbial composition of human stool. Microbiome 3:33
Fouhy F, Deane J, Rea MC, O’Sullivan Ó, Ross RP et al (2015) The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations. PLoS One 10:e0119355
Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G et al (2013) Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504:446–450
Gorzelak MA, Gill SK, Tasnim N, Ahmadi-Vand Z, Jay M, Gibson DL (2015) Methods for improving human gut microbiome data by reducing variability through sample processing and storage of stool. PLoS One 10:e0134802
Hale VL, Tan CL, Knight R, Amato KR (2015) Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks. J Microbiol Methods 113:16–26
Hale VL, Tan CL, Niu K, Yang Y, Cui D et al (2016) Effects of field conditions on fecal microbiota. J Microbiol Methods 130:180–188
Hallmaier-Wacker LK, Lueert S, Roos C, Knauf S (2018) The impact of storage buffer, DNA extraction method, and polymerase on microbial analysis. Sci Rep 8:6292
Hanya G, Noma N, Agetsuma N (2003) Altitudinal and seasonal variations in the diet of Japanese macaques in Yakushima. Primates 44:51–59
Hanya G, Naito S, Namioka E, Ueda Y, Sato Y, Pastrana JA, He T, Yan X, Saito M, Costa RFP, Allanic M, Honda T, Kurihara Y, Yumoto T, Hayakawa T (2017) Morphometric and genetic determination of age class and sex for fecal pellets of Sika deer (Cervus nippon). Mammal Study 42:1–8
Hayaishi S, Kawamoto Y (2002) Fecal genotyping of mitochondrial DNA polymorphism and fecal age-class estimation of Macaca fuscata yakui: a preliminary report. Mammal Sci 42:161–166 (in Japanese)
Hayaishi S, Kawamoto Y (2006) Low genetic diversity and biased distribution of mitochondrial DNA haplotypes in the Japanese macaque (Macaca fuscata yakui) on Yakushima Island. Primates 47:158–164
Hiergeist A, Reischl U, Gessner A, Priority Program 1656 Intestinal Microbiota Consortium/quality assessment participants (2016) Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability. Int J Med Microbiol 306:334–342
Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17:377–386
Inoue E, Akomo-Okoue EF (2015) Application of DNA bar coding techniques to mammal inventories in the African rain forest: droppings may inform us of the owners. Tropics 23:137–150
Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33:511–518
Kawamoto Y, Takemoto H, Higuchi S, Sakamaki T, Hart JA et al (2013) Genetic structure of wild bonobo populations: diversity of mitochondrial DNA and geographical distribution. PLoS One 8:e59660
Kim SW, Suda W, Kim S, Oshima K, Fukuda S et al (2013) Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing. DNA Res 20:241–253
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C et al (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:e1
Krynak KL, Burke DJ, Martin RA, Dennis PM (2017) Gut microbiome composition is associated with cardiac disease in zoo-housed western lowland gorillas (Gorilla gorilla gorilla). FEMS Microbiol Lett 364:fnx149
Kurihara Y, Hanya G (2017) Comparison of energy balance between two different-sized groups of Japanese macaques (Macaca fuscata yakui). Primates 58:413–422
Lampa S, Henle K, Klenke R, Hoehn M, Gruber B (2013) How to overcome genotyping errors in non-invasive genetic mark-recapture population size estimation—a review of available methods illustrated by a case study. J Wildl Manag 77:1490–1511
Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR et al (2008) Evolution of mammals and their gut microbes. Science 320:1647–1651
Li W, Fu L, Niu B, Wu S, Wooley J (2012) Ultrafast clustering algorithms for metagenomic sequence analysis. Brief Bioinform 13:656–668
Longmire JL, Maltbie M, Baker RJ (1997) Use of ‘lysis buffer’ in DNA isolation and its implication for museum collections. Occ Pap Mus Texas Tech Univ 163:1–3
Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235
Ma J, Prince AL, Bader D, Hu M, Ganu R et al (2014) High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model. Nat Commun 5:3889
Menke S, Gillingham MA, Wilhelm K, Sommer S (2017) Home-made cost effective preservation buffer is a better alternative to commercial preservation methods for microbiome research. Front Microbiol 8:102
Metzler-Zebeli BU, Lawlor PG, Magowan E, Zebeli Q (2016) Effect of freezing conditions on fecal bacterial composition in pigs. Animals 6:E18
Moeller AH, Degnan PH, Pusey AE, Wilson ML, Hahn BH, Ochman H (2012) Chimpanzees and humans harbour compositionally similar gut enterotypes. Nat Commun 3:1179
Moeller AH, Caro-Quintero A, Mjungu D, Georgiev AV, Lonsdorf EV et al (2016a) Cospeciation of gut microbiota with hominids. Science 353:380–382
Moeller AH, Foerster S, Wilson ML, Pusey AE, Hahn BH, Ochman H (2016b) Social behavior shapes the chimpanzee pan-microbiome. Sci Adv 2:e1500997
Morin PA, Chambers KE, Boesch C, Vigilant L (2001) Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus). Mol Ecol 10:1835–1844
Muegge BD, Kuczynski J, Knights D, Clemente JC, Gonzalez A et al (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332:970–974
Muiños-Bühl A, González-Recio O, Muñoz M, Óvilo C, García-Casco J, Fernández AI (2018) Evaluating protocols for porcine faecal microbiome recollection, storage and DNA extraction: from the farm to the lab. Curr Microbiol 75:651–657
Nsubuga AM, Robbins MM, Roeder AD, Morin PA, Boesch C, Vigilant L (2004) Factors affecting the amount of genomic DNA extracted from ape faeces and the identification of an improved sample storage method. Mol Ecol 13:2089–2094
Perofsky AC, Lewis RJ, Abondano LA, Di Fiore A, Meyers LA (2017) Hierarchical social networks shape gut microbial composition in wild Verreaux’s sifaka. Proc Biol Sci 284:20172274
Pielou EC (1966) Shannon’s formula as a measure of specific diversity: its use and misuses. Am Nat 104:463–465
Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650
Qin J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65
Ranjan R, Rani A, Metwally A, McGee HS, Perkins DL (2016) Analysis of the microbiome: advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun 469:967–977
Sanders JG, Powell S, Kronauer DJ, Vasconcelos HL, Frederickson ME, Pierce NE (2014) Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes. Mol Ecol 23:1268–1283
Sawada A, Sato H, Inoue E, Otani Y, Hanya G (2014) Mycophagy among Japanese macaques in Yakushima: fungal species diversity and behavioral patterns. Primates 55:249–257
Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B et al (2017) Assessment of variation in microbial community amplicon sequencing by the microbiome quality control (MBQC) project consortium. Nat Biotechnol 35:1077–1086
Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS et al (2017) Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. Science 357:802–806
Sommer F, Bäckhed F (2013) The gut microbiota—masters of host development and physiology. Nat Rev Microbiol 11:227–238
Song SJ, Amir A, Metcalf JL, Amato KR, Xu ZZ et al (2016) Preservation methods differ in fecal microbiome stability, affecting suitability for field studies. mSystems 1:e00021
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
Sun B, Wang X, Bernstein S, Huffman MA, Xia D et al (2016) Marked variation between winter and spring gut microbiota in free-ranging Tibetan macaques (Macaca thibetana). Sci Rep 6:26035
Tanabe AS, Toju H (2013) Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants. PLoS One 8:e76910
Tremaroli V, Bäckhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489:242–249
Tremblay J, Singh K, Fern A, Kirton ES, He S et al (2015) Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol 6:771
Tsuji Y (2010) Regional, temporal, and interindividual variation in the feeding ecology of Japanese macaques. In: Nakagawa N, Nakamichi M, Sugiura H (eds) The Japanese macaques. Springer, Tokyo, pp 99–127
Tung J, Barreiro LB, Burns MB, Grenier JC, Lynch J et al (2015) Social networks predict gut microbiome composition in wild baboons. Elife 4:e05224
Vallet D, Petit EJ, Gatti S, Levréro F, Ménard N (2008) A new 2CTAB/PCI method improves DNA amplification success from faeces of Mediterranean (Barbary macaques) and tropical (lowland gorillas) primates. Conserv Genet 9:677–680
Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 73:5261–5267
Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA et al (2012) Impact of training sets on classification of high-throughput bacterial 16S rRNA gene surveys. ISME J 6:94–103
Wrangham RW (1974) Artificial feeding of chimpanzees and baboons in their natural habitat. Anim Behav 22:83–93
Yamagiwa J (2008) History and present scope of field studies on Macaca fuscata yakui at Yakushima Island, Japan. Int J Primatol 29:49–64
Yamagiwa J, Hill DA (1998) Intraspecific variation in the social organization of Japanese macaques: past and present scope of field studies in natural habitats. Primates 39:257–273
