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

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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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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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Effect of Electron Donor to Sulfate Ratio on Mercury Methylation in Floodplain Sediments under Saturated Flow Conditions
Desrochers, K. A. N., Paulson, K. M. A., Ptacek, C. J., Blowes, D. W., & Gould, W. D. (2015) · Geomicrobiology Journal · doi:10.1080/01490451.2015.1035818 · Cited by 13
“The operational taxonomic units (OTUs) were defined at 97% homology after removal of singleton sequences (Dowd et al. 2008; Edgar 2010).”
Method
Activities and Prevalence of Proteobacteria Members Colonizing Echinacea purpurea Fully Account for Macrophage Activation Exhibited by Extracts of This Botanical
Haron, M. H., Tyler, H. L., Pugh, N. D., Moraes, R. M., Maddox, V. L., Jackson, C. R., & Pasco, D. S. (2016) · Planta Medica · doi:10.1055/s-0042-108590 · Cited by 13
“Bacterial tag-encoded FLX amplicon 454 pyrosequencing (bTEFAP) [17] was conducted on the 16S rRNA 735 bp product of each sample through a dedicated sequencing facility (MR DNA).”
Lactic Acid Fermentation of Human Excreta for Agricultural Application
Andreev, N. (2017) · CRC Press eBooks · doi:10.1201/9781315116280 · Cited by 13
Bacterial Community Survey of Solenopsis invicta Buren (Red imported fire Ant) Colonies in the Presence and Absence of Solenopsis invicta Virus (SINV)
Powell, C. M., Hanson, J. D., & Bextine, B. R. (2014) · Current Microbiology · doi:10.1007/s00284-014-0626-4 · Cited by 13
Structured variable selection with q-values
Garcia, T. P., Müller, S., Carroll, R. J., Dunn, T. N., Thomas, A. P., Adams, S. H., Pillai, S. D., & Walzem, R. L. (2013) · Biostatistics · doi:10.1093/biostatistics/kxt012 · Cited by 13
Microbial Diversity of Ground Beef Products in South Korean Retail Market Analyzed by PCR-DGGE and 454 Pyrosequencing
Koo, O. K., Kim, H. J., Baker, C. A., Park, S. H., & Ricke, S. C. (2016) · Food Biotechnology · doi:10.1080/08905436.2015.1137216 · Cited by 13
“Dowd et al. (2008) identified Clostridium, Porphyromonas, Bacteroides, Ruminococcus, Alistipes, Lachnospira, and Prevotella spp as prevalent in the fecal cattle samples from the Holstein dairy cattle.”
Background
Thermophilic Archaeal Diversity and Methanogenesis from El Tatio Geyser Field, Chile
Plenge, M. F., Engel, A. S., Omelon, C. R., & Bennett, P. C. (2016) · Geomicrobiology Journal · doi:10.1080/01490451.2016.1168496 · Cited by 13
“Amplified products were prepared for tag pyrosequencing by the Research and Testing Laboratory (Lubbock, TX, USA) using a Roche 454 Genome Sequences system following their protocols (www. researchandtesting.com; Dowd et al. 2008).”
Method
Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology
Verma, M. (2016) · Technology in Cancer Research & Treatment · doi:10.1177/1533034616645219 · Cited by 14
Data Analysis Methodology
Edalat, F. D., & Abdi, M. R. (2017) · International series in management science/operations research/International series in operations research & management science · doi:10.1007/978-3-319-64143-0_7 · Cited by 13
Hypersaline microbial fuel cell equipped with an oxygen-reducing microbial cathode
Rimboud, M., Etcheverry, L., Barakat, M., Achouak, W., Bergel, A., & Délia, M.-L. (2021) · Bioresource Technology · doi:10.1016/j.biortech.2021.125448 · Cited by 13
Microbial Ecology Pushes Frontiers in Biotechnology
Kouzuma, A., & Watanabe, K. (2014) · Microbes and Environments · doi:10.1264/jsme2.me2901rh · Cited by 13
“, 16S rRNA genes) fragments PCR-amplified from community metagenomes (5).”
Background
The Fecal Microbial Communities of Dairy Cattle Shedding Shiga Toxin–Producing Escherichia coli or Campylobacter jejuni
Dong, H.-J., Kim, W.-H., An, J.-U., Kim, J., & Cho, S. (2016) · Foodborne Pathogens and Disease · doi:10.1089/fpd.2016.2121 · Cited by 13
“Among the top 10 predominant genera in this study, Clostridium and Alistipes are considered ubiquitous genera in dairy cattle (Dowd et al. , 2008), and Peptostreptococcaceae (the family containing Romboutsia and Asaccharospora ) and Turicibacter are the core taxa in beef cattle (Shanks et al. ,…”
No effect of Bt Cry1Ie toxin on bacterial diversity in the midgut of the Chinese honey bees, Apis cerana cerana (Hymenoptera, Apidae)
Jia, H., Dai, P., Geng, L., Jack, C., Li, Y., Wu, Y., Diao, Q., & Ellis, J. D. (2017) · Scientific Reports · doi:10.1038/srep41688 · Cited by 13
Microbial taxa related to natural hydrogen and methane emissions in serpentinite-hosted hyperalkaline springs of New Caledonia
Quéméneur, M., Mei, N., Monnin, C., Postec, A., Guasco, S., Jeanpert, J., Maurizot, P., Pelletier, B., & Erauso, G. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1196516 · Cited by 12
A walk on the dirt: soil microbial forensics from ecological theory to the crime lab
Jurkevitch, É., & Pasternak, Z. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa053 · Cited by 14
Monomorphic pathogens: The case of Candidatus Xenohaliotis californiensis from abalone in California, USA and Baja California, Mexico
Cicala, F., Moore, J. D., Cáceres-Martı́nez, J., del Río-Portilla, M. Á., Hernández-Rodríguez, M., Vásquez‐Yeomans, R., & Rocha‐Olivares, A. (2018) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2018.03.012 · Cited by 12
Soil microbial community changes associated with ground cover management in cultivation of Ducasse banana (Musa sp. ABB, Pisang Awak subgroup) and suppression of Fusarium oxysporum
Rames, E. K., Pattison, A. B., Czislowski, E., & Smith, M. K. (2018) · Australasian Plant Pathology · doi:10.1007/s13313-018-0578-4 · Cited by 12
Determining an optimal pool size for testing beef herds for Johne’s disease in Australia
Ly, A., Dhand, N. K., Sergeant, E. S. G., Marsh, I. B., & Plain, K. M. (2019) · PLoS ONE · doi:10.1371/journal.pone.0225524 · Cited by 12
“PCR inhibitors may arise due to the complex nature of the faecal matrix of ruminants, with a variety of endogenous (high diversity of bacterial species) and exogenous (herbivorous matter) components [20, 21].”
Background
Temporal Dynamics of Chronic Inflammation on the Cecal Microbiota in IL-10-/- Mice
Overstreet, A.-M. C., Ramer‐Tait, A. E., Suchodolski, J. S., Hostetter, J. M., Wang, C., Jergens, A. E., Phillips, G. J., & Wannemuehler, M. J. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2020.585431 · Cited by 12
“The data reduction analysis was performed as previously described (51).”
MethodInfluential
A systematized review and qualitative synthesis of potential risk factors associated with the occurrence of non‐O157 Shiga toxin‐producing Escherichia coli (STEC) in the primary production of cattle
Withenshaw, S. M., Smith, R. P., Davies, R. H., Smith, A. E. O., Gray, E., & Rodgers, J. D. (2022) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12929 · Cited by 12
Associations Between Gut Microbes and Social Behavior in Healthy 2-Year-Old Children
Delgadillo, D. R., Pressman, S. D., Christian, L. M., Galley, J. D., & Bailey, M. T. (2022) · Psychosomatic Medicine · doi:10.1097/psy.0000000000001103 · Cited by 13
“Bacterial tag-encoded FLX-amplicon pyrosequencing (bTEFAP) was performed (42,43).”
Method
Habitability and Biosignature Formation in Simulated Martian Aqueous Environments
Macey, M. C., Ramkissoon, N. K., Cogliati, S., Toubes-Rodrigo, M., Stephens, B. P., Kucukkilic-Stephens, E., Schwenzer, S. P., Pearson, V. K., Preston, L. J., & Olsson‐Francis, K. (2022) · Astrobiology · doi:10.1089/ast.2021.0197 · Cited by 12
“The PCR products were sequenced using the Illumina Miseq Platform by Molecular Research LP (Texas, USA) and processed using a customized pipeline (Dowd et al., 2008a, 2008b).”
Temporal and Spatial Variation Characteristics and Influencing Factors of Bacterial Community in Urban Landscape Lakes
Zhang, Y., Wang, M., Cheng, W., Huang, C., Ren, J., Zhai, H., & Li, N. (2023) · Microbial Ecology · doi:10.1007/s00248-023-02249-z · Cited by 12
“Bacteroidetes are associated with the intestinal microflora of many mammals, some of which are considered effective fecal indicators, and their high abundance may be due to direct discharge of residential wastewater, which may contain pollutants such as nitrate, ammonia, and feces [38].”
Background
Assessment of potential anaerobic biotransformation of organic pollutants in sediment caps
Smith, A., Kirisits, M. J., & Reible, D. D. (2012) · New Biotechnology · doi:10.1016/j.nbt.2012.06.003 · Cited by 12
Evaluation of soluble corn fiber on chemical composition and nitrogen-corrected true metabolizable energy and its effects on in vitro fermentation and in vivo responses in dogs
Panasevich, M. R., Kerr, K. R., Serao, M. C. R., de Godoy, M. R. C., Guérin‐Deremaux, L., Lynch, G. L., Wils, D., Dowd, S. E., Fahey, G. C., Jr., Swanson, K. S., et al. (2015) · Journal of Animal Science · doi:10.2527/jas.2014-8425 · Cited by 12
Hard-to-heal diabetes-related foot ulcers: current challenges and future prospects
Nubé, V. L., Frank, G., White, J., Stubbs, S., Nannery, S., Pfrunder, L., Twigg, S. M., & McLennan, S. (2016) · Chronic Wound Care Management and Research · doi:10.2147/cwcmr.s84990 · Cited by 12
“80 How this new information will be translated to more targeted therapeutics is not as yet clear, although a recent study has shown that personalized treatment based on type of bacteria present, identified by DNA analysis, can improve wound healing and at reduced cost.”
Novel bacterial diversity is enriched with chloroperoxidase-reacted organic matter under anaerobic conditions.
Lim, M. L., Brooks, M. D., Boothe, M. A., & Krzmarzick, M. J. (2018) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiy050 · Cited by 12
Novel methods for pathogen control in livestock pre-harvest: an update * *Mandatory Disclaimer: Proprietary or brand names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies no approval of the product, or exclusion of others that may be suitable.
Callaway, T. R., Anderson, R. C., Edrington, T. S., Genovese, K. J., Harvey, R. B., Poole, T. L., & Nisbet, D. J. (2013) · Elsevier eBooks · doi:10.1533/9780857098740.4.275 · Cited by 12
Procaryotic Diversity and Hydrogenotrophic Methanogenesis in an Alkaline Spring (La Crouen, New Caledonia)
Quéméneur, M., Mei, N., Monnin, C., Postec, A., Wils, L., Joseph, M., Guasco, S., Pelletier, B., & Erauso, G. (2021) · Microorganisms · doi:10.3390/microorganisms9071360 · Cited by 12
“Bacterial and archaeal 16S rRNA gene V4 hypervariable regions were amplified by PCR using the 515F/806R universal primer set [48], with a barcode on the forward primer, as previously described by Dowd et al., and were sequenced by the MiSeq Illumina platform of the Molecular Research Laboratory (Shallowater, TX, USA)…”
Method
Microbial source tracking of fecal contamination in stormwater runoff
Sherchan, S. P., Shahin, S. A., Alarcon, J., Brosky, H., Potter, C., & Dada, A. C. (2022) · Journal of Water and Health · doi:10.2166/wh.2022.286 · Cited by 11
Recovery of soil microbial diversity and functions along a tropical montane forest disturbance gradient
Sniegocki, R., Moon, J. B., Rutrough, A. L., Gireneus, J., Seelan, J., Farmer, M., Weindorf, D., & Naithani, K. (2022) · Frontiers in Environmental Science · doi:10.3389/fenvs.2022.853686 · Cited by 11
“We received final operational taxonomic units (OTUs) that were assigned based on 97% similarity and followed the proprietary MR DNA analysis pipeline (Dowd et al., 2008) from the Molecular Research Laboratory (MR DNA, Shallowater, TX, United States).”
Method
Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes
Liang, J., Ali, S., Lv, C., Yang, H., Zhao, X., Ni, X., Li, C., Danzeng, B., Wang, Y., & Quan, G. (2023) · Frontiers in Endocrinology · doi:10.3389/fendo.2023.1194425 · Cited by 11
Relationship between bubble motion, nitrogen removal, and microbial community characteristics in black-odorous water under micro-aeration: Effects of aeration rate
Lu, C., Wen, C., Zhang, B., Wang, J., Ren, J., & Ju, K. (2025) · Journal of Water Process Engineering · doi:10.1016/j.jwpe.2025.107117 · Cited by 11
Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel‐contaminated soil
Arbel, J., King, C. K., Raymond, B., Winsley, T. J., & Mengersen, K. L. (2015) · Ecology and Evolution · doi:10.1002/ece3.1493 · Cited by 11
“Genomic DNA extracted from samples was sequenced on a 454 Titanium FLX instrument (Roche, Branford, CT) at the Research and Testing facility (Lubbock, TX) using the universal bacterial primers 28F and 519R (Dowd et al. 2008).”
Method
Altered Transcription of Murine Genes Induced in the Small Bowel by Administration of Probiotic Strain Lactobacillus rhamnosus HN001
Tannock, G. W., Taylor, C., Lawley, B., Loach, D. M., Gould, M. L., Dunn, A. C., McLellan, A. D., Black, M. A., McNoe, L. A., Dekker, J., et al. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00336-14 · Cited by 11
Co-invasion hypothesis explains microbial community structure changes in upland streams affected by riparian invader
McInerney, P., & Rees, G. N. (2017) · Freshwater Science · doi:10.1086/692068 · Cited by 11
“Data analysis A proprietary analysis pipeline (MR DNA) was used for 16S rRNA gene sequence analysis (Dowd et al. 2008).”
Method
Arbuscular Mycorrhizal Fungal Communities in Organic and Conventional Onion Crops in the Columbia Basin of the Pacific Northwest United States
Knerr, A. J., Wheeler, D. L., Schlatter, D., Sharma‐Poudyal, D., du Toit, L. J., & Paulitz, T. C. (2018) · Phytobiomes Journal · doi:10.1094/pbiomes-05-18-0022-r · Cited by 11
Bacterial community analysis on the different mucosal immune inductive sites of gastrointestinal tract in Bactrian camels
Zhang, W., Yao, W., He, W., Li, J.-F., Wu, X., Chen, Z., Liu, L., & Wang, W. (2020) · PLoS ONE · doi:10.1371/journal.pone.0239987 · Cited by 11
“In this study, the common dominant bacteria colonized the mucosa surface of the ALNA and ileal PPs were the same as in the intestine of other animals, such as dromedary [20], Bactrian camel [19], cattle [32], sheep [33] and horse [34].”
Background
HCH Removal in a Biochar-Amended Biofilter
Amirbekov, A., Mamirova, A., Ševců, A., Špánek, R., & Hrabák, P. (2021) · Water · doi:10.3390/w13233396 · Cited by 11
“The V4 region of the bacterial 16S rDNA gene was amplified using the primers 530F (5′TGCCAGCMGCNGCGG3′) and 802R (5′TACNVGGGTATCTAATCC3′) in a final volume of 50 μL [42,43].”
Method
Chryseobacterium faecale sp. nov., isolated from camel feces
Son, Y., Min, J., & Park, W. (2022) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.005405 · Cited by 11
Diversity and abundance of bacterial and fungal communities in rhizospheric soil from smallholder banana producing agroecosystems in Kenya
Wahome, C. N., Maingi, J. M., Ombori, O., Njeru, E. M., Muthini, M., & Kimiti, J. M. (2023) · Frontiers in Horticulture · doi:10.3389/fhort.2023.1061456 · Cited by 11
Planktonic Growth ofPseudomonas aeruginosaaround a Dual-Species Biofilm Supports the Growth ofFusobacterium nucleatumwithin That Biofilm
Wang, J. C., Cordero, J., Sun, Y., Aranke, M., Wolcott, R. D., Colmer‐Hamood, J. A., & Hamood, A. N. (2017) · International Journal of Otolaryngology · doi:10.1155/2017/3037191 · Cited by 11
“2 million DNA capture beads and then amplified by emulsion PCR using the same primer set with added linker A and 8-bp barcode sequences at the 5-end of 28F (primer 28F-A 5-CCATCTCATCCCTGCGTGTCTCCGACTCAG-barcode-GAGTTTGATCNTGGCTCAG-3) and biotin and the linker B sequence added to the 5-end of 519R (primer 519R-B 5-Biot…”
Method
Phylogenetic diversity and metabolic potential of microbiome of natural healing clay from Chamliyal (J&K)
Sharma, S., Grewal, S., & Vakhlu, J. (2018) · Archives of Microbiology · doi:10.1007/s00203-018-1549-4 · Cited by 11
“coli rRNA and Candida albicans, respectively (Dowd et al. 2008).”
Shotgun metagenomics reveals differences in antibiotic resistance genes among bacterial communities in Western Balkans glacial lakes sediments
Filipić, B., Novović, K., Studholme, D. J., Malešević, M., Mirković, N., Kojić, M., & Jovčić, B. (2020) · Journal of Water and Health · doi:10.2166/wh.2020.227 · Cited by 11
Microfiber structure for enhanced immobilization of nitrifying bacteria in a post-nitrification reactor
Svobodová, L., Havlíček, K., Nechanická, M., Špánek, R., Sirková, B. K., Lenfeldová, I., Ondřej, L., Moučková, E., & Lederer, T. (2021) · Environmental Technology & Innovation · doi:10.1016/j.eti.2021.101373 · Cited by 11
Differentiating the role of different-sized microorganisms in peptide decomposition during incubations using size-fractioned coastal seawater
Liu, S., Riesen, A., & Liu, Z. (2015) · Journal of Experimental Marine Biology and Ecology · doi:10.1016/j.jembe.2015.07.004 · Cited by 11

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 › Animal Science and Zoology › 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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