Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

Dowd, Scot E; Callaway, Todd R; Wolcott, Randall D; Sun, Yan; McKeehan, Trevor; Hagevoort, Robert G; Edrington, Thomas S

doi:10.1186/1471-2180-8-125

Cited by 1,121Gut microbiota and healthRuminant Nutrition and Digestive PhysiologyAnimal Nutrition and Physiology

Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

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Dowd, Scot E, Callaway, Todd R, Wolcott, Randall D, Sun, Yan, McKeehan, Trevor, Hagevoort, Robert G, Edrington, Thomas S·2008·BMC Microbiology

DOI 10.1186/1471-2180-8-125PMC PMC2515157

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Abstract

BACKGROUND: The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows. RESULTS: Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae). CONCLUSION: Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing.

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Prevotella, Bacteroides, Ruminococcus, Faecalibacterium, Roseburia and Clostridium are consistently identified in fecal samples from ruminants and are considered part of the core microbiota.
“Prevotella, Bacteroides, Ruminococcus, Faecalibacterium, Roseburia and Clostridium are consistently identified in fecal samples from ruminants and are considered part of the core microbiota (Dowd et al., 2008; Durso et al., 2012).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Dowd et al., 2008

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The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses
Větrovský, T., & Baldrián, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057923 · Cited by 1,201 · see citing works
Exposure to a social stressor alters the structure of the intestinal microbiota: Implications for stressor-induced immunomodulation
Bailey, M. T., Dowd, S. E., Galley, J. D., Hufnagle, A. R., Allen, R. G., & Lyte, M. (2011) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2010.10.023 · Cited by 1,123 · see citing works
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
Segata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C., & Izard, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r42 · Cited by 1,076 · see citing works
Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil
Banerjee, S., Kirkby, C. A., Schmutter, D., Bissett, A., Kirkegaard, J. A., & Richardson, A. E. (2016) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2016.03.017 · Cited by 1,050 · see citing works
Pyrosequencing study of fecal microflora of autistic and control children
Finegold, S. M., Dowd, S. E., Gontcharova, V., Liu, C., Henley, K. E., Wolcott, R. D., Youn, E., Summanen, P. H., Granpeesheh, D., Dixon, D., et al. (2010) · Anaerobe · doi:10.1016/j.anaerobe.2010.06.008 · Cited by 977 · see citing works
Analysis of the lung microbiome in the “healthy” smoker and in COPD.
Erb-Downward, J. R., Thompson, D. L., Han, M. K., Freeman, C. M., McCloskey, L., Schmidt, L. A., Young, V. B., Toews, G. B., Curtis, J. L., Sundaram, B., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016384 · Cited by 973 · see citing works
Exploring the bovine rumen bacterial community from birth to adulthood
Jami, E., Israel, A., Kotser, A., & Mizrahi, I. (2013) · The ISME Journal · doi:10.1038/ismej.2013.2 · Cited by 963 · see citing works
Active and total microbial communities in forest soil are largely different and highly stratified during decomposition
Baldrián, P., Kolařík, M., Štursová, M., Kopecký, J., Brabcová, V., Větrovský, T., Žifčáková, L., Šnajdr, J., Rídl, J., Vlček, Č., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.95 · Cited by 865 · see citing works
Composition of fungal and bacterial communities in forest litter and soil is largely determined by dominant trees
Urbanová, M., Šnajdr, J., & Baldrián, P. (2015) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2015.02.011 · Cited by 679 · see citing works
Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency
Jami, E., White, B. A., & Mizrahi, I. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085423 · Cited by 588 · see citing works
Dynamic Gut Microbiome across Life History of the Malaria Mosquito Anopheles gambiae in Kenya
Wang, Y., Gilbreath, T. M., Kukutla, P., Yan, G., & Xu, J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024767 · Cited by 586 · see citing works
Composition and Similarity of Bovine Rumen Microbiota across Individual Animals
Jami, E., & Mizrahi, I. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033306 · Cited by 572 · see citing works
Polymicrobial Nature of Chronic Diabetic Foot Ulcer Biofilm Infections Determined Using Bacterial Tag Encoded FLX Amplicon Pyrosequencing (bTEFAP)
Dowd, S. E., Wolcott, R. D., Sun, Y., McKeehan, T., Smith, E., & Rhoads, D. D. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003326 · Cited by 562 · see citing works
Large‐scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest
Öpik, M., METSIS, M. L., Daniell, T. J., Zobel, M., & Moora, M. (2009) · New Phytologist · doi:10.1111/j.1469-8137.2009.02920.x · Cited by 557 · see citing works
Diversity of the human skin microbiome early in life
Capone, K. A., Dowd, S. E., Stamatas, G. N., & Nikolovski, J. (2011) · Journal of Investigative Dermatology · doi:10.1038/jid.2011.168 · Cited by 532 · see citing works
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Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers
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Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use
Acosta‐Martínez, V., Dowd, S. E., Sun, Y., & Allen, V. G. (2008) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2008.07.022 · Cited by 486 · see citing works
Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future
Huws, S. A., Creevey, C. J., Oyama, L. B., Mizrahi, I., Denman, S. E., Popova, M., Muñoz-Tamayo, R., Forano, E., Waters, S. M., Hess, M., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02161 · Cited by 487 · see citing works
Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats
Handl, S., Dowd, S. E., García-Mazcorro, J. F., Steiner, J. M., & Suchodolski, J. S. (2011) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2011.01058.x · Cited by 445 · see citing works
Seasonal Variability in Bacterial and Fungal Diversity of the Near-Surface Atmosphere
Bowers, R. M., Clements, N. S., Emerson, J., Wiedinmyer, C., Hannigan, M., & Fierer, N. (2013) · Environmental Science & Technology · doi:10.1021/es402970s · Cited by 420 · see citing works
Changes in Gut Microbiota in Rats Fed a High Fat Diet Correlate with Obesity-Associated Metabolic Parameters
Lecomte, V., Kaakoush, N. O., Maloney, C., Raipuria, M., Huinao, K. D., Mitchell, H. M., & Morris, M. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0126931 · Cited by 418 · see citing works
Characterization of the Core Rumen Microbiome in Cattle during Transition from Forage to Concentrate as Well as during and after an Acidotic Challenge
Petri, R. M., Schwaiger, T., Penner, G. B., Beauchemin, K. A., Forster, R. J., McKinnon, J. J., & McAllister, T. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0083424 · Cited by 410 · see citing works
Exposure to a social stressor disrupts the community structure of the colonic mucosa-associated microbiota
Galley, J. D., Nelson, M. C., Yu, Z., Dowd, S. E., Walter, J., Kumar, P., Lyte, M., & Bailey, M. T. (2014) · BMC Microbiology · doi:10.1186/1471-2180-14-189 · Cited by 398 · see citing works
Impact of Biochar Application to Soil on the Root-Associated Bacterial Community Structure of Fully Developed Greenhouse Pepper Plants
Kolton, M., Harel, Y. M., Pasternak, Z., Gräber, E. R., Elad, Y., & Cytryn, E. J. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.00148-11 · Cited by 394 · see citing works
Antibiotics, Bacteria, and Antibiotic Resistance Genes: Aerial Transport from Cattle Feed Yards via Particulate Matter
McEachran, A. D., Blackwell, B. R., Hanson, J. D., Wooten, K. J., Mayer, G. D., Cox, S. B., & Smith, P. N. (2015) · Environmental Health Perspectives · doi:10.1289/ehp.1408555 · Cited by 372 · see citing works
Diversity and function of the avian gut microbiota
Kohl, K. D. (2012) · Journal of Comparative Physiology B · doi:10.1007/s00360-012-0645-z · Cited by 367 · see citing works
Community structures of fecal bacteria in cattle from different animal feeding operations
Shanks, O. C., Kelty, C. A., Archibeque, S., Jenkins, M., Newton, R. J., McLellan, S. L., Huse, S. M., & Sogin, M. L. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02988-10 · Cited by 359 · see citing works
Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes
Kim, M., Morrison, M., & Yu, Z. (2010) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2010.10.020 · Cited by 358 · see citing works
Bacterial Biofilm Infection Detected in Breast Implant–Associated Anaplastic Large-Cell Lymphoma
Hu, H., Johani, K., Almatroudi, A., Vickery, K., Natta, B. W. V., Kadin, M. E., Brody, G. S., Clemens, M. W., Cheah, C. Y., Lade, S., et al. (2016) · Plastic & Reconstructive Surgery · doi:10.1097/prs.0000000000002010 · Cited by 349 · see citing works
Ecology of Root Colonizing Massilia (Oxalobacteraceae)
Ofek, M., Hadar, Y., & Minz, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040117 · Cited by 348 · see citing works
Stressor Exposure Disrupts Commensal Microbial Populations in the Intestines and Leads to Increased Colonization by <i>Citrobacter rodentium</i>
Bailey, M. T., Dowd, S. E., Parry, N. M. A., Galley, J. D., Schauer, D. B., & Lyte, M. (2010) · Infection and Immunity · doi:10.1128/iai.00862-09 · Cited by 335 · see citing works
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The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing
Pechal, J. L., Crippen, T. L., Benbow, M. E., Tarone, A. M., Dowd, S. E., & Tomberlin, J. K. (2013) · International Journal of Legal Medicine · doi:10.1007/s00414-013-0872-1 · Cited by 328 · see citing works
Assessment of bacterial diversity in the cattle tick Rhipicephalus (Boophilus) microplusthrough tag-encoded pyrosequencing
Andreotti, R., de León, A. Á. P., Dowd, S. E., Guerrero, F. D., Bendele, K. G., & Scoles, G. A. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-6 · Cited by 321 · see citing works
Influence of hydraulic regimes on bacterial community structure and composition in an experimental drinking water distribution system
Douterelo, I., Sharpe, R. L., & Boxall, J. B. (2012) · Water Research · doi:10.1016/j.watres.2012.09.053 · Cited by 300 · see citing works
Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes
Sanders, J. G., Powell, S., Kronauer, D. J. C., Vasconcelos, H. L. D., Frederickson, M. E., & Pierce, N. E. (2013) · Molecular Ecology · doi:10.1111/mec.12611 · Cited by 291 · see citing works
Current status of cow dung as a bioresource for sustainable development
Gupta, K. K., Aneja, K. R., & Rana, D. (2016) · Bioresources and Bioprocessing · doi:10.1186/s40643-016-0105-9 · Cited by 295 · see citing works
Determinants of bacterial communities in C anadian agroforestry systems
Banerjee, S., Baah‐Acheamfour, M., Carlyle, C. N., Bissett, A. B., Richardson, A. E., Siddique, T., Bork, E. W., & Chang, S. X. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.12986 · Cited by 289 · see citing works
Responses of the functional structure of soil microbial community to livestock grazing in the T ibetan alpine grassland
Yang, Y., Wu, L., Lin, Q., Yuan, M., Xu, D., Yu, H., Hu, Y., Duan, J., Li, X., He, Z., et al. (2012) · Global Change Biology · doi:10.1111/gcb.12065 · Cited by 293 · see citing works
Effects of biochar and compost amendments on soil physico-chemical properties and the total community within a temperate agricultural soil
Abujabhah, I. S., Bound, S., Doyle, R., & Bowman, J. P. (2015) · Applied Soil Ecology · doi:10.1016/j.apsoil.2015.10.021 · Cited by 292 · see citing works
Prevotella: A Key Player in Ruminal Metabolism
Betancur-Murillo, C. L., Aguilar-Marín, S. B., & Jovel, J. (2022) · Microorganisms · doi:10.3390/microorganisms11010001 · Cited by 283 · see citing works
Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing1
Callaway, T. R., Dowd, S. E., Edrington, T. S., Anderson, R. C., Krueger, N., Bauer, N., Kononoff, P. J., & Nisbet, D. J. (2010) · Journal of Animal Science · doi:10.2527/jas.2010-2900 · Cited by 275 · see citing works
A study of ticks and tick-borne livestock pathogens in Pakistan
Karim, S., Budachetri, K., Mukherjee, N., Williams, J., Kausar, A., Hassan, M. J., Adamson, S. W., Dowd, S. E., Apanskevich, D., Arijo, A. G., et al. (2017) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0005681 · Cited by 272 · see citing works
The effect of diet and exercise on intestinal integrity and microbial diversity in mice
Campbell, S. C., Wisniewski, P. J., Noji, M., McGuinness, L. R., Häggblom, M. M., Lightfoot, S. A., Joseph, L. B., & Kerkhof, L. J. (2016) · PLOS ONE · doi:10.1371/journal.pone.0150502 · Cited by 268 · see citing works
Legacy effects of soil moisture on microbial community structure and N2O emissions
Banerjee, S., Helgason, B. L., Wang, L., Winsley, T. J., Ferrari, B. C., & Siciliano, S. D. (2015) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2015.12.004 · Cited by 266 · see citing works
Top-Down Systems Biology Modeling of Host Metabotype−Microbiome Associations in Obese Rodents
Waldram, A., Holmes, E. C., Wang, Y., Rantalainen, M., Wilson, I. D., Tuohy, K. M., McCartney, A. L., Gibson, G. R., & Nicholson, J. K. (2009) · Journal of Proteome Research · doi:10.1021/pr8009885 · Cited by 266 · see citing works
Shift in the microbial community composition of surface water and sediment along an urban river
Wang, L., Zhang, J., Li, H., Yang, H., Peng, C., Peng, Z., & Lu, L. (2018) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2018.01.203 · Cited by 262 · see citing works
Dysregulated hepatic bile acids collaboratively promote liver carcinogenesis
Xie, G., Wang, X., Huang, F., Zhao, A., Chen, W., Yan, J., Zhang, Y., Lei, S., Ge, K., Zheng, X., et al. (2016) · International Journal of Cancer · doi:10.1002/ijc.30219 · Cited by 252 · see citing works
Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota
Goddard, A. F., Staudinger, B. J., Dowd, S. E., Joshi-Datar, A., Wolcott, R. D., Aitken, M. L., Fligner, C. L., & Singh, P. K. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1107435109 · Cited by 254 · see citing works
Microbiome–metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model
Mao, S., Huo, W., & Zhu, W. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.12724 · Cited by 257 · see citing works
Pseudomonas aeruginosa: Infections, Animal Modeling, and Therapeutics
Wood, S. J., Kuzel, T. M., & Shafikhani, S. H. (2023) · Cells · doi:10.3390/cells12010199 · Cited by 267 · see citing works
Dominance of sulfur-fueled iron oxide reduction in low-sulfate freshwater sediments
Hansel, C. M., Lentini, C. J., Tang, Y., Johnston, D. T., Wankel, S. D., & Jardine, P. M. (2015) · The ISME Journal · doi:10.1038/ismej.2015.50 · Cited by 247 · see citing works
Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community
Brabcová, V., Nováková, M., Davidova, A. N., & Baldrián, P. (2016) · New Phytologist · doi:10.1111/nph.13849 · Cited by 247 · see citing works
Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis
Mancabelli, L., Milani, C., Lugli, G. A., Turroni, F., Cocconi, D., van Sinderen, D., & Ventura, M. (2017) · FEMS Microbiology Ecology · doi:10.1093/femsec/fix153 · Cited by 240 · see citing works
Characterization of microbial community structure during continuous anaerobic digestion of straw and cow manure
Sun, L., Pope, P. B., Eijsink, V. G. H., & Schnürer, A. (2015) · Microbial Biotechnology · doi:10.1111/1751-7915.12298 · Cited by 232 · see citing works
Comparison of the Compositions of the Stool Microbiotas of Infants Fed Goat Milk Formula, Cow Milk-Based Formula, or Breast Milk
Tannock, G. W., Lawley, B., Munro, K., Pathmanathan, S. G., Zhou, S. J., Makrides, M., Gibson, R. A., Sullivan, T., Prosser, C. G., Lowry, D. J., et al. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.03910-12 · Cited by 230 · see citing works
The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing
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Distinctly altered gut microbiota in the progression of liver disease
Xie, G., Wang, X., Liu, P., Wei, R., Chen, W., Rajani, C., Hernandez, B. Y., Alegado, R., Dong, B., Li, D., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.8466 · Cited by 219 · see citing works
The analysis of oral microbial communities of wild-type and toll-like receptor 2-deficient mice using a 454 GS FLX Titanium pyrosequencer
Chun, J., Kim, K. Y., Lee, J.-H., & Choi, Y. (2010) · BMC Microbiology · doi:10.1186/1471-2180-10-101 · Cited by 225 · see citing works
Changes in the Rumen Epimural Bacterial Diversity of Beef Cattle as Affected by Diet and Induced Ruminal Acidosis
Petri, R. M., Schwaiger, T., Penner, G. B., Beauchemin, K. A., Forster, R. J., McKinnon, J. J., & McAllister, T. A. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.03983-12 · Cited by 218 · see citing works
Bacterial community composition and structure in an Urban River impacted by different pollutant sources
Ibekwe, A. M., Ma, J., & Murinda, S. E. (2016) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2016.05.168 · Cited by 214 · see citing works
Comparative Analysis of Microbial Profiles in Cow Rumen Fed with Different Dietary Fiber by Tagged 16S rRNA Gene Pyrosequencing
Thoetkiattikul, H., Mhuantong, W., Laothanachareon, T., Tangphatsornruang, S., Pattarajinda, V., Eurwilaichitr, L., & Champreda, V. (2013) · Current Microbiology · doi:10.1007/s00284-013-0336-3 · Cited by 209 · see citing works
Nitrogenase Gene Amplicons from Global Marine Surface Waters Are Dominated by Genes of Non-Cyanobacteria
Farnelid, H., Andersson, A. F., Bertilsson, S., Al‐Soud, W. A., Hansen, L. H., Sørensen, S. J., Steward, G. F., Hagström, Å., & Riemann, L. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019223 · Cited by 209 · see citing works
Molecular Characterisation of Gastrointestinal Microbiota of Children With Autism (With and Without Gastrointestinal Dysfunction) and Their Neurotypical Siblings
Gondalia, S. V., Palombo, E. A., Knowles, S. R., Cox, S. B., Meyer, D., & Austin, D. W. (2012) · Autism Research · doi:10.1002/aur.1253 · Cited by 208 · see citing works
Pyrosequencing Reveals the Influence of Organic and Conventional Farming Systems on Bacterial Communities
Li, R., Khafipour, E., Krause, D. O., Entz, M. H., de Kievit, T. R., & Fernando, W. G. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0051897 · Cited by 207 · see citing works
Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores
Sanders, J. G., Beichman, A. C., Roman, J., Scott, J. J., Emerson, D., McCarthy, J. J., & Girguis, P. R. (2015) · Nature Communications · doi:10.1038/ncomms9285 · Cited by 205 · see citing works
A review of feeding supplementary nitrate to ruminant animals: nitrate toxicity, methane emissions, and production performance
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Studying Bacterial Multispecies Biofilms: Where to Start?
Røder, H. L., Sørensen, S. J., & Burmølle, M. (2016) · Trends in Microbiology · doi:10.1016/j.tim.2016.02.019 · Cited by 198 · see citing works
The Effects of a Probiotic Yeast on the Bacterial Diversity and Population Structure in the Rumen of Cattle
Pinloche, E., McEwan, N. R., Marden, J. P., Bayourthe, C., Auclair, E., & Newbold, C. J. (2013) · PLoS ONE · doi:10.1371/journal.pone.0067824 · Cited by 202 · see citing works
Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables
Jackson, C. R., Randolph, K. C., Osborn, S. L., & Tyler, H. L. (2013) · BMC Microbiology · doi:10.1186/1471-2180-13-274 · Cited by 202 · see citing works
Intensive care unit environmental surfaces are contaminated by multidrug-resistant bacteria in biofilms: combined results of conventional culture, pyrosequencing, scanning electron microscopy, and confocal laser microscopy
Hu, H., Johani, K., Gosbell, I. B., Jacombs, A., Almatroudi, A., Whiteley, G. S., Deva, A. K., Jensen, S. O., & Vickery, K. (2015) · Journal of Hospital Infection · doi:10.1016/j.jhin.2015.05.016 · Cited by 198 · see citing works
Culture Enriched Molecular Profiling of the Cystic Fibrosis Airway Microbiome
Sibley, C. D., Grinwis, M. E., Field, T. R., Eshaghurshan, C. S., Faria, M. M. P., Dowd, S. E., Parkins, M. D., Rabin, H. R., & Surette, M. G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022702 · Cited by 194 · see citing works
Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience
Mandaković, D., Rojas, C., Maldonado, J. E., Latorre, M., Travisany, D., Delage, E., Bihouée, A., Jean, G., Díaz, F. P., Fernández-Gómez, B., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-23931-0 · Cited by 188 · see citing works
Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer
de Oliveira, M. N. V., Jewell, K. A., Freitas, F. S., Benjamin, L. A., Tótola, M. R., Borges, A. C., Moraes, C. A., & Suen, G. (2013) · Veterinary Microbiology · doi:10.1016/j.vetmic.2013.02.013 · Cited by 184 · see citing works
Gut microbiome composition is associated with temperament during early childhood
Christian, L. M., Galley, J. D., Hade, E. M., Schoppe-Sullivan, S., Kamp Dush, C., & Bailey, M. T. (2015) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2014.10.018 · Cited by 191 · see citing works
Maternal Obesity Is Associated with Alterations in the Gut Microbiome in Toddlers
Galley, J. D., Bailey, M. T., Dush, C. M. K., Schoppe‐Sullivan, S. J., & Christian, L. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113026 · Cited by 180 · see citing works
Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons
Shepherd, M. L., Swecker, W. S., Jensen, R. V., & Ponder, M. A. (2011) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2011.02434.x · Cited by 177 · see citing works
Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rRNA amplicons
López‐Velasco, G., Welbaum, G. E., Boyer, R. R., Mane, S. P., & Ponder, M. A. (2011) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2011.04969.x · Cited by 176 · see citing works
Functional screening of abundant bacteria from acidic forest soil indicates the metabolic potential of Acidobacteria subdivision 1 for polysaccharide decomposition
Lladó, S., Žifčáková, L., Větrovský, T., Eichlerová, I., & Baldrián, P. (2015) · Biology and Fertility of Soils · doi:10.1007/s00374-015-1072-6 · Cited by 176 · see citing works
Assessing the Impact of Copper and Zinc Oxide Nanoparticles on Soil: A Field Study
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Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and Titanium amplicon pyrosequencing and metagenomic approaches
Wolcott, R. D., Gontcharova, V., Sun, Y., & Dowd, S. E. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-226 · Cited by 174 · see citing works
Black Box Chimera Check (B2C2): a Windows-Based Software for Batch Depletion of Chimeras from Bacterial 16S rRNA Gene Datasets
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Diversity and composition of the bacterial community in the feces of cattle and goats
Mahayri, T. M. (n.d.) · UnissResearch (Università degli Studi di Sassari)

Authors: Dowd, S. E., Callaway, T. R., Wolcott, R. D., Sun, Y., McKeehan, T., Hagevoort, R. G., & Edrington, T. S.
Affiliations: Agricultural Research Service (US)
Corresponding author: Dowd, Scot E
ORCID: Dowd, Scot E
Callaway, Todd R
Edrington, Thomas S
Venue: BMC Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2008
Volume: 8
Issue: 1
Pages: 125
ISSN: 1471-2180 (ISSN-L)
DOI: 10.1186/1471-2180-8-125
PMC: PMC2515157
OpenAlex: W2105807803
Cited by: 1,121
References: 80
Citations by year: 2026: 16 · 2025: 23 · 2024: 32 · 2023: 32 · 2022: 45 · 2021: 65 · 2020: 52 · 2019: 60 · 2018: 68 · 2017: 105 · 2016: 116 · 2015: 121 · 2014: 129 · 2013: 99 · 2012: 75
FWCI: 11.37
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: BMC Microbiology (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders: U.S. Department of Agriculture
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
Keywords: fecal microbiota, bacterial diversity, dairy cattle, Clostridium, Bacteroides, Ruminococcus, Lachnospiraceae, foodborne pathogens, Salmonella, Campylobacter, gut microbiota
MeSH terms: Animals, Bacteria, Cattle, DNA, Bacterial, DNA, Ribosomal, Feces, Female, RNA, Ribosomal, 16S, Polymerase Chain Reaction, Sequence Analysis, DNA, Gastrointestinal Tract, Biodiversity

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Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

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