2,253
Views
2
CrossRef citations to date
0
Altmetric
Review

Using microbiome information to understand and improve animal performance

ORCID Icon & ORCID Icon
Pages 899-913 | Received 30 Nov 2021, Accepted 07 May 2022, Published online: 19 May 2022

References

  • Abbas HF, AL Musawi IH. 2016. Evaluation three methods of the extraction and purification of bacterial DNA of Gram positive and Gram negative bacteria. World J Exp Biosci. 4:899–65.
  • Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Grüning BA, et al. 2018. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46(W1):W537–W544.
  • Ahlawat S, Asha  , Sharma KK. 2020. Gut–organ axis: a microbial outreach and networking. Lett Appl Microbiol. 72(6):636–668.
  • Alazzeh AY, Sultana H, Beauchemin KA, Wang Y, Holo H, Harstad OM, McAllister TA. 2012. Using strains of propionibacteria to mitigate methane emissions in vitro. Acta Agric Scand A Anim Sci. 62(4):263–272.
  • Allaband C, McDonald D, Vázquez-Baeza Y, Minich JJ, Tripathi A, Brenner DA, Loomba R, Smarr L, Sandborn WJ, Schnabl B, et al. 2019. Microbiome 101: studying, analyzing, and interpreting gut microbiome data for clinicians. Clin Gastroenterol Hepatol. 17(2):218–230.
  • Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, et al. 2017. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome. BMC Microbiol. 17(1):19.
  • Anyansi C, Straub TJ, Manson AL, Earl AM, Abeel T. 2020. Computational methods for strain-level microbial detection in colony and metagenome sequencing data. Front Microbiol. 11:1925.
  • Araujo G, Yunta C, Terré M, Mereu A, Ipharraguerre I, Bach A. 2015. Intestinal permeability and incidence of diarrhea in newborn calves. J Dairy Sci. 98(10):7309–7317.
  • Ayad M, Benallou B, Saim M, Smadi M, Meziane T. 2013. Impact of feeding yeast culture on milk yield, milk components, and blood components in Algerian dairy herds. J Vet Sci Technol. 4(2):1–5.
  • Bach A. 2012. Ruminant nutrition symposium: optimizing performance of the offspring: nourishing and managing the dam and postnatal calf for optimal lactation, reproduction, and immunity. J Anim Sci. 90(6):1835–1845.
  • Banos S, Lentendu G, Kopf A, Wubet T, Glöckner FO, Reich M. 2018. A comprehensive fungi-specific 18S rRNA gene sequence primer toolkit suited for diverse research issues and sequencing platforms. BMC Microbiol. 18(1):190.
  • Bashiardes S, Zilberman-Schapira G, Elinav E. 2016. Use of metatranscriptomics in microbiome research. Bioinform Biol Insights. 10:BBI.S34610.
  • Bergstrom KSB, Kissoon-Singh V, Gibson DL, Ma C, Montero M, Sham HP, Ryz N, Huang T, Velcich A, Finlay BB, et al. 2010. Muc2 protects against lethal infectious colitis by disassociating pathogenic and commensal bacteria from the colonic mucosa. PLoS Pathog. 6(5):e1000902.
  • Berry D, Crowley J. 2013. Cell biology symposium: genetics of feed efficiency in dairy and beef cattle. J Anim Sci. 91(4):1594–1613.
  • Besser TE, Gay CC. 1994. The importance of colostrum to the health of the neonatal calf. Vet Clin North Am Food Anim Practi. 10(1):107–117.
  • Bharti R, Grimm DG. 2021. Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform. 22(1):178–193.
  • Biddle A, Stewart L, Blanchard J, Leschine S. 2013. Untangling the genetic basis of fibrolytic specialization by lachnospiraceae and ruminococcaceae in diverse gut communities. Diversity. 5(3):627–640.
  • Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 10(1):57–59.
  • Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 37(8):852–857.
  • Brulc JM, Antonopoulos DA, Berg Miller ME, Wilson MK, Yannarell AC, Dinsdale EA, Edwards RE, Frank ED, Emerson JB, Wacklin P, et al. 2009. Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA. 106(6):1948–1953.
  • Buffa G, Mangia NP, Cesarani A, Licastro D, Sorbolini S, Pulina G, Nudda A. 2020. Agroindustrial by-products from tomato, grape and myrtle given at low dosage to lactating dairy ewes: effects on rumen parameters and microbiota. Ital J Anim Sci. 19(1):1462–1471.
  • Bush LJ, Staley TE. 1980. Absorption of colostral immunoglobulins in newborn calves1. J Dairy Sci. 63(4):672–680.
  • Callahan BJ, McMurdie PJ, Holmes SP. 2017. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. Isme J. 11(12):2639–2643.
  • Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 13(7):581–583.
  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 7(5):335–336.
  • Carberry CA, Kenny DA, Han S, McCabe MS, Waters SM. 2012. Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Appl Environ Microbiol. 78(14):4949–4958.
  • Casals-Pascual C, González A, Vázquez-Baeza Y, Song SJ, Jiang L, Knight R. 2020. Microbial diversity in clinical microbiome studies: sample size and statistical power considerations. Gastroenterology. 158(6):1524–1528.
  • Chao A. 1984. Nonparametric estimation of the number of classes in a population. Scand J Stat. 11(4):265–270.
  • Chappidi S, Villa EC, Cantarel BL. 2019. Using mothur to determine bacterial community composition and structure in 16S ribosomal RNA datasets. Curr Protoc Bioinformatics. 67(1):e83.
  • Cheng CS, Wei HK, Wang P, Yu HC, Zhang XM, Jiang SW, Peng J. 2019. Early intervention with faecal microbiota transplantation: an effective means to improve growth performance and the intestinal development of suckling piglets. Animal. 13(3):533–541.
  • Clemmons BA, Martino C, Powers JB, Campagna SR, Voy BH, Donohoe DR, Gaffney J, Embree MM, Myer PR. 2019. Rumen bacteria and serum metabolites predictive of feed efficiency phenotypes in beef cattle. Sci Rep. 9(1):19265.
  • Cunningham-Rundles C. 2001. Physiology of IgA and IgA deficiency. J Clin Immunol. 21(5):303–309.
  • Ding X, Lan W, Liu G, Ni H, Gu JD. 2019. Exploring possible associations of the intestine bacterial microbiome with the pre-weaned weight gaining performance of piglets in intensive pig production. Sci Rep. 9(1):15534. https://doi.org/10.1038/s41598-019-52045-4.
  • Ding SY, Rincon MT, Lamed R, Martin JC, McCrae SI, Aurilia V, Shoham Y, Bayer EA, Flint HJ. 2001. Cellulosomal scaffoldin-like proteins from Ruminococcus flavefaciens. J Bacteriol. 183(6):1945–1953.
  • Durso LM, Miller DN, Schmidt TB, Callaway T. 2017. Tracking bacteria through the entire gastrointestinal tract of a beef steer. https://dx.doi.org/10.2134/ael2017.05.0016.
  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 27(16):2194–2200.
  • Enss ML, Grosse-Siestrup H, Schmidt-Wittig U, Gärtner K. 1992. Changes in colonic mucins of germfree rats in response to the introduction of a "normal" rat microbial flora. Rat colonic mucin. J Exp Anim Sci. 35(3):110–119.
  • Enss ML, Schmidt-Wittig U, Müller H, Mai UE, Coenen M, Hedrich HJ. 1996. Response of germfree rat colonic mucous cells to peroral endotoxin application. Eur J Cell Biol. 71(1):99–104.
  • Espeche MC, Pellegrino M, Frola I, Larriestra A, Bogni C, Nader-Macías MEF. 2012. Lactic acid bacteria from raw milk as potentially beneficial strains to prevent bovine mastitis. Anaerobe. 18(1):103–109.
  • Ewaschuk JB, Diaz H, Meddings L, Diederichs B, Dmytrash A, Backer J, Langen ML-v, Madsen KL. 2008. Secreted bioactive factors from Bifidobacterium infantis enhance epithelial cell barrier function. Am J Physiol Gastrointest Liver Physiol. 295(5):G1025–G1034.
  • FAO/WHO. 2006. Probiotics in food. Health and nutritional properties and guidelines for evaluation. Rome, Italy: FAO/WHO.
  • Fernando SC, Purvis HT, Najar FZ, Sukharnikov LO, Krehbiel CR, Nagaraja TG, Roe BA, De SU. 2010. Rumen microbial population dynamics during adaptation to a high-grain diet [Article. Appl Environ Microbiol. 76(22):7482–7490.
  • Fidler G, Tolnai E, Stagel A, Remenyik J, Stundl L, Gal F, Biro S, Paholcsek M. 2020. Tendentious effects of automated and manual metagenomic DNA purification protocols on broiler gut microbiome taxonomic profiling. Sci Rep. 10(1):3419.
  • Finneran E, Crosson P, O'kiely P, Shalloo L, Forristal D, Wallace M. 2012. Stochastic simulation of the cost of home-produced feeds for ruminant livestock systems. J Agric Sci. 150(1):123–139.
  • Flint HJ, Bayer EA. 2008. Plant cell wall breakdown by anaerobic microorganisms from the mammalian digestive tract. Ann NY Acad Sci. 1125(1):280–288.
  • Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA. 2008. Polysaccharide utilization by gut bacteria: Potential for new insights from genomic analysis. Nat Rev Microbiol. 6(2):121–131.
  • Gibson GR, Roberfroid MB. 1995. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr. 125(6):1401–1412.
  • Goodwin S, McPherson JD, McCombie WR. 2016. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 17(6):333–351.
  • Greub G. 2012. Culturomics: a new approach to study the human microbiome. Clin Microbiol Infect. 18(12):1157–1159.
  • Han S, Van Treuren W, Fischer CR, Merrill BD, DeFelice BC, Sanchez JM, Higginbottom SK, Guthrie L, Fall LA, Dodd D, et al. 2021. A metabolomics pipeline for the mechanistic interrogation of the gut microbiome. Nature. 595(7867):415–420.
  • Heikema AP, Horst-Kreft D, Boers SA, Jansen R, Hiltemann SD, De Koning W, Kraaij R, De Ridder MAJ, Van Houten CB, Bont LJ, et al. 2020. Comparison of illumina versus nanopore 16S rRNA gene sequencing of the human nasal microbiota. Genes. 11(9):1105.
  • Henderson G, Cox F, Kittelmann S, Miri VH, Zethof M, Noel SJ, Waghorn GC, Janssen PH. 2013. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PLoS One. 8(9):e74787.
  • Herd R, Arthur P. 2009. Physiological basis for residual feed intake. J Anim Sci. 87(14):E64–E71.
  • Hobson PN, Stewart CS. 2012. The rumen microbial ecosystem. Berlin, Germany: Springer Science & Business Media.
  • Illumina 2013. 16S metagenomic sequencing library preparation. Part # 15044223 Rev. B. [accessed]. https://support.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf
  • Iyer SS, Cheng G. 2012. Role of interleukin 10 transcriptional regulation in inflammation and autoimmune disease. Crit Rev Immunol. 32(1):23–63.
  • Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, et al. 2019. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 10, 5029. https://doi.org/10.1038/s41467-019-13036-1.
  • Kim H, Kim S, Jung S. 2020. Instruction of microbiome taxonomic profiling based on 16S rRNA sequencing. J Microbiol. 58(3):193–205.
  • Kittelmann S, Kirk MR, Jonker A, McCulloch A, Janssen PH, Schloss PD. 2015. Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen. Appl Environ Microbiol. 81(21):7470–7483.
  • Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41(1):e1.
  • Koetsier G, Cantor E. 2019. A practical guide to analyzing nucleic acid concentration and purity with microvolume spectrophotometers. Ipswich (MA): New England Biolabs Inc.
  • Kogut MH. 2019. The effect of microbiome modulation on the intestinal health of poultry. Anim Feed Sci Technol. 250:32–40.
  • Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS. 2003. Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol Rev. 27(5):663–693.
  • Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, Bittar F, Fournous G, Gimenez G, Maraninchi M, et al. 2012. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect. 18(12):1185–1193.
  • Legendre P, Borcard D, Peres-Neto PR. 2005. Analyzing beta diversity: partitioning the spatial variation of community composition data. Ecol Monogr. 75(4):435–450.
  • Li F, Hitch TCA, Chen Y, Creevey CJ, Guan LL. 2019. Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. Microbiome. 7(1):6.
  • Liang G, Malmuthuge N, Bao H, Stothard P, Griebel PJ, Guan LL. 2016. Transcriptome analysis reveals regional and temporal differences in mucosal immune system development in the small intestine of neonatal calves. BMC Genomics. 17(1):602.
  • Lourenco JM, Callaway TR, Kieran TJ, Glenn TC, McCann JC, Stewart RL. 2019. Analysis of the rumen microbiota of beef calves supplemented during the suckling phase. Front Microbiol. 10:1131.
  • Lourenco JM, Hampton RS, Johnson HM, Callaway TR, Rothrock MJ, Azain MJ. 2021. The effects of feeding antibiotic on the intestinal microbiota of weanling pigs. Front Vet Sci. 8:601394.
  • Lourenco JM, Kieran TJ, Seidel DS, Glenn TC, Silveira M, Callaway TR, Stewart RL. Jr. 2020. Comparison of the ruminal and fecal microbiotas in beef calves supplemented or not with concentrate. PLoS One. 15(4):e0231533.
  • Lourenco JM, Maia FJ, Bittar JHJ, Segers JR, Tucker JJ, Campbell BT, Stewart RL. 2020. Utilization of exogenous enzymes in beef cattle creep feeds. J Appl Anim Res. 48(1):70–77.
  • Lozupone C, Knight R. 2005. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol. 71(12):8228–8235.
  • Lucena-Aguilar G, Sánchez-López AM, Barberán-Aceituno C, Carrillo-Ávila JA, López-Guerrero JA, Aguilar-Quesada R. 2016. DNA source selection for downstream applications based on DNA quality indicators analysis. Biopreserv Biobank. 14(4):264–270.
  • Magurran AE. 2003. Measuring biological diversity. Hoboken (NJ): John Wiley & Sons.
  • Mahalanabis M, Al-Muayad H, Kulinski MD, Altman D, Klapperich CM. 2009. Cell lysis and DNA extraction of gram-positive and gram-negative bacteria from whole blood in a disposable microfluidic chip. Lab Chip. 9(19):2811–2817.
  • Malmuthuge N, Guan LL. 2017. Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation. J Anim Sci Biotechnol. 8(1):8.
  • Marchiando AM, Graham WV, Turner JR. 2010. Epithelial barriers in homeostasis and disease. Annu Rev Pathol. 5(1):119–144.
  • Martin KJ, Rygiewicz PT. 2005. Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol. 5(1):28.
  • Mattiello F, Verbist B, Faust K, Raes J, Shannon WD, Bijnens L, Thas O. 2016. A web application for sample size and power calculation in case-control microbiome studies. Bioinformatics. 32(13):2038–2040.
  • McAllister T. 2000. Learning more about rumen bugs: genetic and environmental factors affecting rumen bugs. Southern Alberta Beef Rev. 2(1).
  • McCann JC, Wickersham TA, Loor JJ. 2014. High-throughput methods redefine the rumen microbiome and its relationship with nutrition and metabolism. Bioinform Biol Insights. 8:109–125. eng.
  • McMurdie PJ, Holmes S. 2013. Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. 8(4):e61217.
  • Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al. 2008. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 9(1):386.
  • Miyauchi E, O’Callaghan J, Buttó LF, Hurley G, Melgar S, Tanabe S, Shanahan F, Nally K, O'Toole PW. 2012. Mechanism of protection of transepithelial barrier function by Lactobacillus salivarius: strain dependence and attenuation by bacteriocin production. Am J Physiol Gastrointest Liver Physiol. 303(9):G1029–G1041.
  • Mizrahi I. 2013. 21 Rumen symbioses. In Rosenberg E, editor. The prokaryotes. 4 ed. Berlin, Germany: Springer.
  • Mintert J. 2021. The importance of managing hog operation feed costs. West Lafayette (IN): Purdue University Center for Commercial Agriculture; p. 2.
  • Mulder IE, Schmidt B, Lewis M, Delday M, Stokes CR, Bailey M, Aminov RI, Gill BP, Pluske JR, Mayer CD, et al. 2011. Restricting microbial exposure in early life negates the immune benefits associated with gut colonization in environments of high microbial diversity. PLoS One. 6(12):e28279.
  • Myer PR, Smith TP, Wells JE, Kuehn LA, Freetly HC. 2015. Rumen microbiome from steers differing in feed efficiency. PLoS One. 10(6):e0129174.
  • Nagaraja TG, Chengappa MM. 1998. Liver abscesses in feedlot cattle: a review. J Anim Sci. 76(1):287–298.
  • Nakajima A, Vogelzang A, Maruya M, Miyajima M, Murata M, Son A, Kuwahara T, Tsuruyama T, Yamada S, Matsuura M, et al. 2018. IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria. J Exp Med. 215(8):2019–2034.
  • Nygaard AB, Tunsjø HS, Meisal R, Charnock C. 2020. A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes. Sci Rep. 10, 3209 (2020). https://doi.org/10.1038/s41598-020-59771-0.
  • O’Hara E, Neves ALA, Song Y, Guan LL. 2020. The role of the gut microbiome in cattle production and health: driver or passenger? Annu Rev Anim Biosci. 8(1):199–220.
  • Okumura R, Takeda K. 2018. Maintenance of intestinal homeostasis by mucosal barriers. Inflamm Regen. 38(1):5.
  • Pham VT, Dold S, Rehman A, Bird JK, Steinert RE. 2021. Vitamins, the gut microbiome and gastrointestinal health in humans. Nutr Res. 95:35–53.
  • Pollock J, Glendinning L, Wisedchanwet T, Watson M, Liu S-J. 2018. The madness of microbiome: attempting to find consensus “ best practice” for 16S microbiome studies. Appl Environ Microbiol. 84(7):e02627–02617.
  • Rajasekaran SA, Beyenbach KW, Rajasekaran AK. 2008. Interactions of tight junctions with membrane channels and transporters. Biochim Biophys Acta (BBA) - Biomembran. 1778(3):757–769.
  • Rakotoarivonina H, Larson MA, Morrison M, Girardeau JP, Gaillard-Martinie B, Forano E, Mosoni P. 2005. The Ruminococcus albus pilA1-pilA2 locus: expression and putative role of two adjacent pil genes in pilus formation and bacterial adhesion to cellulose. Microbiology (Reading). 151(Pt 4):1291–1299.
  • Reyer H, Oster M, McCormack UM, Muráni E, Gardiner GE, Ponsuksili S, Lawlor PG, Wimmers K. 2020. Host-microbiota interactions in ileum and caecum of pigs divergent in feed efficiency contribute to nutrient utilization. Microorganisms. 8(4):563.
  • Rothrock MJ, Jr, Hiett KL, Gamble J, Caudill AC, Cicconi-Hogan KM, Caporaso JG. 2014. A hybrid DNA extraction method for the qualitative and quantitative assessment of bacterial communities from poultry production samples. JoVE. (94):e52161.
  • Sawada N, Murata M, Kikuchi K, Osanai M, Tobioka H, Kojima T, Chiba H. 2003. Tight junctions and human diseases. Med Electron Microsc. 36(3):147–156.
  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 75(23):7537–7541.
  • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Bolchacova E, Voigt K, Crous PW, et al. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109(16):6241–6246.
  • Shabat SKB, Sasson G, Doron-Faigenboim A, Durman T, Yaacoby S, Berg Miller ME, White BA, Shterzer N, Mizrahi I. 2016. Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. ISME J. 10(12):2958–2972.
  • Shang Y, Kumar S, Oakley B, Kim WK. 2018. Chicken gut microbiota: importance and detection technology. Front Vet Sci. 5:254.
  • Shroff KE, Meslin K, Cebra JJ. 1995. Commensal enteric bacteria engender a self-limiting humoral mucosal immune response while permanently colonizing the gut. Infect Immun. 63(10):3904–3913.
  • Smits HH, Engering A, van der Kleij D, de Jong EC, Schipper K, van Capel TMM, Zaat BAJ, Yazdanbakhsh M, Wierenga EA, van Kooyk Y, et al. 2005. Selective probiotic bacteria induce IL-10-producing regulatory T cells in vitro by modulating dendritic cell function through dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin. J Allergy Clin Immunol. 115(6):1260–1267.
  • Stanley D, Denman SE, Hughes RJ, Geier MS, Crowley TM, Chen H, Haring VR, Moore RJ. 2012. Intestinal microbiota associated with differential feed conversion efficiency in chickens. Appl Microbiol Biotechnol. 96(5):1361–1369.
  • Stanley D, Geier MS, Chen H, Hughes RJ, Moore RJ. 2015. Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences. BMC Microbiol. 15(1):51.
  • Stillie R, Farooq SM, Gordon JR, Stadnyk AW. 2009. The functional significance behind expressing two IL-8 receptor types on PMN. J Leukoc Biol. 86(3):529–543.
  • Sultana R, McBain AJ, O’Neill CA. 2013. Strain-dependent augmentation of tight-junction barrier function in human primary epidermal keratinocytes by Lactobacillus and bifidobacterium lysates. Appl Environ Microbiol. 79(16):4887–4894.
  • Sylvester JT, Karnati SKR, Yu Z, Morrison M, Firkins JL. 2004. Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J Nutr. 134(12):3378–3384.
  • Szentkuti L, Riedesel H, Enss ML, Gaertner K, von Engelhardt W. 1990. Pre-epithelial mucus layer in the colon of conventional and germ-free rats. Histochem J. 22(9):491–497.
  • Thijs S, Op De Beeck M, Beckers B, Truyens S, Stevens V, Van Hamme JD, Weyens N, Vangronsveld J. 2017. Comparative evaluation of four bacteria-specific primer pairs for 16S rRNA gene surveys. Front Microbiol. 8:494.
  • Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 2007. The human microbiome project. Nature. 449(7164):804–810.
  • USDA/APHIS. 1995. Feedlot health management report: part II: cattle on feed evaluation. Fort Collins (CO): USDA/APHIS/Veterinary Services, Centers for Epidemiology and Animal Health; p. 0195.
  • Wallace RJ, Rooke JA, Duthie C-A, Hyslop JJ, Ross DW, McKain N, de Souza SM, Snelling TJ, Waterhouse A, Roehe R. 2015. Archaeal abundance in post-mortem ruminal digesta may help predict methane emissions from beef cattle. Sci Rep. 4(1):5892.
  • Wallace RJ, Sasson G, Garnsworthy PC, Tapio I, Gregson E, Bani P, Huhtanen P, Bayat AR, Strozzi F, Biscarini F, et al. 2019. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Sci Adv. 5(7):eaav8391.
  • Welch CB, Lourenco JM, Davis DB, Krause TR, Carmichael MN, Rothrock MJ, Pringle TD, Callaway TR. 2020. The impact of feed efficiency selection on the ruminal, cecal, and fecal microbiomes of Angus steers from a commercial feedlot. J Anim Sci. 98(7):skaa230, https://doi.org/10.1093/jas/skaa230.
  • Welch CB, Lourenco JM, Krause TR, Seidel DS, Fluharty FL, Pringle TD, Callaway TR. 2021. Evaluation of the fecal bacterial communities of Angus steers with divergent feed efficiencies across the lifespan from weaning to slaughter. Front Vet Sci. 8(694):597405.
  • Willis AD. 2019. Rarefaction, alpha diversity, and statistics perspective. Front Microbiol. 10: 2407.
  • Wisener LV, Sargeant JM, O’Connor AM, Faires MC, Glass-Kaastra SK. 2015. The use of direct-fed microbials to reduce shedding of Escherichia coli O157 in beef cattle: a systematic review and meta-analysis. Zoonoses Public Health. 62(2):75–89.
  • Xue M, Sun H, Wu X, Guan LL, Liu J, Nojiri H. 2018. Assessment of rumen microbiota from a large dairy cattle cohort reveals the pan and core bacteriomes contributing to varied phenotypes. Appl Environ Microbiol. 84(19):e00970–00918.
  • Xue MY, Sun HZ, Wu XH, Liu JX, Guan LL. 2020. Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance. Microbiome. 8(1):1–19.
  • Yan W, Sun C, Yuan J, Yang N. 2017. Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency. Sci Rep. 7(1):45308.
  • Yang B, Wang Y, Qian PY. 2016. Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC Bioinf. 17(1):135.
  • Yu S, Zhang G, Liu Z, Wu P, Yu Z, Wang J. 2020. Repeated inoculation with fresh rumen fluid before or during weaning modulates the microbiota composition and co-occurrence of the rumen and colon of lambs. BMC Microbiol. 20(1): 29. https://doi.org/10.1186/s12866-020-1716-z.
  • Zehavi T, Probst M, Mizrahi I. 2018. Insights into culturomics of the rumen microbiome. Front Microbiol. 9:1999.
  • Zhang J, Su L, Wang Y, Deng S. 2020. Improved high-throughput sequencing of the human oral microbiome: from illumina to PacBio. Can J Infect Dis Med Microbiol. 2020:6678872.
  • Zhang R, Zhou M, Tu Y, Zhang NF, Deng KD, Ma T, Diao QY. 2016. Effect of oral administration of probiotics on growth performance, apparent nutrient digestibility and stress-related indicators in Holstein calves. J Anim Physiol Anim Nutr (Berl). 100(1):33–38.
  • Zhou M, Hernandez-Sanabria E, Guan LL. 2009. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. Appl Environ Microbiol. 75(20):6524–6533.