Insight into the bacterial gut microbiome of the North American moose (Alces alces)

BMC Microbiology

André-Denis G Wright²  Suzanne L Ishaq¹ 

[1] Department of Animal Science, College of Agriculture and Life Sciences, University of Vermont, 203 Terrill Building, 570 Main Street, Burlington, VT, 05405, USA;Department of Medicine, University of Vermont, 111 Colchester Ave, Burlington, Vermont, 05401, USA

关键词: 16S rRNA;    Vermont;    Rumen;    Gut microbiome;    Colon;   

Others  :  1221751
DOI  :  10.1186/1471-2180-12-212

 received in 2012-05-18, accepted in 2012-09-17,  发布年份 2012

【 摘 要 】

Background

The work presented here provides the first intensive insight into the bacterial populations in the digestive tract of the North American moose (Alces alces). Eight free-range moose on natural pasture were sampled, producing eight rumen samples and six colon samples. Second generation (G2) PhyloChips were used to determine the presence of hundreds of operational taxonomic units (OTUs), representing multiple closely related species/strains (>97% identity), found in the rumen and colon of the moose.

Results

A total of 789 unique OTUs were used for analysis, which passed the fluorescence and the positive fraction thresholds. There were 73 OTUs, representing 21 bacterial families, which were found exclusively in the rumen samples: Lachnospiraceae, Prevotellaceae and several unclassified families, whereas there were 71 OTUs, representing 22 bacterial families, which were found exclusively in the colon samples: Clostridiaceae, Enterobacteriaceae and several unclassified families. Overall, there were 164 OTUs that were found in 100% of the samples. The Firmicutes were the most dominant bacteria phylum in both the rumen and the colon. Microarray data available at ArrayExpress, accession number E-MEXP-3721.

Conclusions

Using PhyloTrac and UniFrac computer software, samples clustered into two distinct groups: rumen and colon, confirming that the rumen and colon are distinct environments. There was an apparent correlation of age to cluster, which will be validated by a larger sample size in future studies, but there were no detectable trends based upon gender.

【 授权许可】

   
2012 Ishaq and Wright; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

【 参考文献 】

• [1]Schwartz CC, Regelin WL, Franzmann AW: Estimates of digestibility of Birch, Willow, and Aspen mixtures in moose. J Wildl Manage 1988, 52:33-37.
• [2]Routledge RG, Roese J: Moose winter diet selection in central Ontario. Alces 2004, 40:95-101.
• [3]Belovsky GE: Food plant selection by a generalist herbivore: the moose. Ecology 1981, 64:1020-1030.
• [4]Belovsky GE, Jordan PA: Sodium dynamics and adaptations of a moose population. J Mammal 1981, 62:613-621.
• [5]Alexander CE: The status and management of moose in Vermont. Alces 1993, 29:187-195.
• [6]Koitzsch KB: Application of a moose habitat suitability index model to Vermont wildlife management units. Alces 2002, 38:89-107.
• [7]2009 Vermont Wildlife Harvest Report. Waterbury, VT: Moose; 2009.
• [8]2007 Vermont Wildlife Harvest Report. Waterbury, VT: Moose; 2007.
• [9]Clauss M, Fritz J, Bayer D, Nygren K, Hammer S, Hatt J-M, Südekum K-H, Hummel J: Physical characteristics of rumen contents in four large ruminants of different feeding type, the addax (Addax nasomaculatus), bison (Bison bison), red deer (Cervus elaphus) and moose (Alces alces). Comp Biochem Physiol, A 2009, 152:398-406.
• [10]Stevens CE, Hume ID: Comparative physiology of the vertebrate digestive system. Second. New York City: Cambridge University; 1995.
• [11]Janssen PH: Influence of hydrogen on rumen methane formation and fermentation balances through microbial growth kinetics and fermentation thermodynamics. Anim Feed Sci Technol 2010, 160:1-22.
• [12]Baldwin RL, Allison MJ: Rumen metabolism. J Anim Sci 1983, 57:461-477.
• [13]Janssen PH, Kirs M: Structure of the archaeal community of the rumen. Appl Envir Microbiol 2008, 74:3619-3625.
• [14]Dehority BA: Microbes in the foregut of arctic ruminants. In Control of digestion and metabolism in ruminants: Proceedings of the Sixth International Symposium on Ruminant Physiology held at Banff, Canada, September 10th-14th, 1984. Edited by Milligan LP, Grovum WL, Dobson A. Englewood Cliffs: Prentice-Hall; 1986:307-325.
• [15]Brodie EL, DeSantis TZ, Parker JPM, Zubietta IX, Piceno YM, Andersen GL: Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci USA 2007, 104:299-304.
• [16]DeSantis TZ, Brodie EL, Moberg JP, Zubietta IX, Piceno YM, Andersen GL: High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 2007, 53:371-383.
• [17]Brodie EL, Desantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL, Hazen TC, Richardson PM, Herman DJ, Tokunaga TK, Wan JM, Firestone MK: Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Envir Microbiol 2006, 72:6288-6298.
• [18]Wu CH, Sercu B, Van de Werfhorst LC, Wong J, DeSantis TZ, Brodie EL, Hazen TC, Holden PA, Andersen GL: Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators. PLoS One 2010, 5:e11285.
• [19]Bissett A, Richardson AE, Baker GC, Wakelin S, Thrall PH: Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales. Molec Ecol 2010, 19:4315-4327.
• [20]Yergeau E, Schoondermark-Stolk SA, Brodie EL, Déjean S, DeSantis TZ, Gonçalves O, Piceno YM, Andersen GL, Kowalchuk GA: Environmental microarray analyses of Antarctic soil microbial communities. ISME J 2009, 3:340-351.
• [21]Godoy-Vitorino F, Goldfarb KC, Brodie EL, Garcia-Amado MA, Michelangeli F, Domınguez-Bello MG: Developmental microbial ecology of the crop of the folivorous hoatzin. ISME J 2010, 4:611-620.
• [22]Maldonado-Contreras A, Goldfarb KC, Godoy-Vitorino F, Karaoz U, Contreras M, Blaser MJ, Brodie EL, Dominguez-Bello MG: Structure of the human gastric bacterial community in relation to Helicobacter pylori status. ISME J 2010, 5:574-579.
• [23]Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, Voolstra CR, Weil E, Andersen GL, Medina M: Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata. ISME J 2009, 3:512-521.
• [24]Neumann LM, Dehority Ba: An investigation of the relationship between fecal and rumen bacterial concentrations in sheep. Zoo Biol 2008, 27:100-108.
• [25]Sundset M-A, Edwards JE, Cheng YF, Senosiain RS, Fraile MN, Northwood KS, Praesteng KE, Glad T, Mathiesen SD, Wright A-DG: Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture. Microb Ecol 2009, 57:335-348.
• [26]Sundset MA, Edwards JE, Cheng YF, Senosiain RS, Fraile MN, Northwood KS, Praesteng KE, Glad T, Mathiesen SD, Wright A-DG: Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea. FEMS Micriobiol Ecol 2009, 70:553-562.
• [27]Hook SE, Steele MA, Northwood KS, Dijkstra J, France J, Wright A-DG, McBride BW: Impact of subacute ruminal acidosis (SARA) adaptation and recovery on the density and diversity of bacteria in the rumen of dairy cows. FEMS Microbiol Ecol 2011, 78:275-284.
• [28]Sundset MA, Praesteng KE, Cann IKO, Mathiesen SD, Mackie RI: Novel rumen bacterial diversity in two geographically separated sub-species of reindeer. Microb Ecol 2007, 54:424-438.
• [29]Præsteng KE, Mackie RI, Cann IK, Mathiesen SD, Sundset MA: Development of a signature probe targeting the 16S-23S rRNA internal transcribed spaces of a ruminal Ruminococcus flavefaciens isolate from reindeer. Beneficial Microbes 2011, 2:47-55.
• [30]Brulc JIM, Antonopoulos DA, Berg Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE: Gene-centric metagenomics of the fiber-adherant bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA 2009, 106:1948-1953.
• [31]Mitsumori M, Ajisaka N, Tajima K, Kajikawa H, Kurihara M: Detection of Proteobacteria from the rumen by PCR using methanotroph-specific primers. Lett Appl Microbiol 2002, 35:251-255.
• [32]Midgley DJ, Greenfield P, Shaw JM, Oytam Y, Li D, Kerr Ca, Hendry P: Reanalysis and simulation suggest a phylogenetic microarray does not accurately profile microbial communities. PLoS One 2012, 7:e33875.
• [33]Wilson KH, Wilson WJ, Radosevich JL, DeSantis TZ, Viswanathan VS, Kuczmarski TA, Andersen GL: High-density microarray of small-subunit ribosomal DNA probes. Appl Envir Microbiol 2002, 68:2535-2541.
• [34]Samsudin AA, Evans PN, Wright A-DG, Al Jassim R: Molecular diversity of the foregut bacteria community in the dromedary camel (Camelus dromedarius). Environ Microbiol 2011, 13:3024-3035.
• [35]Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernández M, Murill C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholt P, Leadbetter JR: Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 2007, 450:560-569.
• [36]Nelson TA, Holmes S, Alekseyenko AV, Shenoy M, Desantis T, Wu CH, Andersen GL, Winston J, Sonnenburg J, Pasricha PJ, Spormann A: PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity. Neurogastroenterol Motil 2011, 23:169-177. e41–2
• [37]Lillehaug A, Bergsjø B, Schau J, Bruheim T, Vikøren T, Handeland K: Campylobacter spp., Salmonella spp., verocytotoxic Escherichia coli, and antibiotic resistance in indicator organisms in wild cervids. Acta Vet Scand 2005, 46:23-32. BioMed Central Full Text
• [38]Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI: An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444:424-438.
• [39]Yu Z, Morrison M: Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 2004, 36:808-812.
• [40]Denman SE, McSweeney CS: Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Micriobiol Ecol 2006, 58:572-582.
• [41]Lane DJ: 16S/23S rRNA sequencing. In Nucleic acid techniques in bacterial systematics. Edited by Stackebrandt E, Goodfellow M. New York City: John Wiley and Sons; 1991:115-175.
• [42]Hamady M, Lozupone C, Knight R: Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J 2010, 4:17-27.
• [43]Lozupone C, Knight R: UniFrac: a new phylogenetic method for comparing microbial communities. Appl Envir Microbiol 2005, 71:8228-8235.