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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Basic local alignment search tool
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Influential
Shotgun Metagenomics Reveals Microbial Diversity, Resistome, and Plasmidome in Dairy Cattle Feces
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“Metagenomic analysis of fecal samples from dairy cattle has been previously documented [32–34].”
Geographic Variation of Bacterial Communities Associated with Cotton Fleahopper, Pseudatomoscelis seriatus1
Fu, Z., Antwi, J., Sword, G. A., Barman, A. K., & Medina, R. F. (2021) · Southwestern Entomologist · doi:10.3958/059.046.0102 · Cited by 3
Dietary Mycotoxins Effects on Nile Tilapia (Oreochromis niloticus) Microbiomes Can Be Mitigated with Addition of Organically Modified Clinoptilolites
Hussein, W., Cholewińska, P., Wojnarowski, K., Szeligowska, N., Hu, F., Greguła‐Kania, M., Rojtinnakorn, J., & Palić, D. (2024) · Microbiology Research · doi:10.3390/microbiolres15040149 · Cited by 3
Gilthead seabream (Sparus aurata) fed with polar lipids from olive oil industry by-products: Shelf-life, microbiological and physicochemical characteristics during storage at 2 °C
Anagnostopoulos, D. A., Martsikalis, P. V., Syropoulou, F., Parlapani, F. F., Polymeros, K., Barkas, D., Papaharisis, L., Antonopoulou, S., & Boziaris, I. S. (2024) · The Microbe · doi:10.1016/j.microb.2024.100222 · Cited by 3
RETRACTED: Malted Barley as a Potential Feed Supplementation for the Reduction of Enteric Methane Emissions, Rumen Digestibility, and Microbiome Community Changes in Laboratory Conditions
Min, B. R., Uyeno, Y., Ismael, H., Abdo, H., Chaudhary, S., Hilaire, M., & Kanyi, V. (2025) · Animals · doi:10.3390/ani15050664 · Cited by 3
“Data quality control and analyses were directed as described by Dowd et al. [29] and Min et al. [21,30].”
Retracted
Sands and environmental conditions impact the abundance and persistence of the fecal indicator bacteria Enterococcus at recreational beaches
Halliday, E. (2012) · doi:10.1575/1912/5461 · Cited by 3
BioDry: An Inexpensive, Low-Power Method to Preserve Aquatic Microbial Biomass at Room Temperature
Tuorto, S. J., Brown, C. M., Bidle, K. D., McGuinness, L. R., & Kerkhof, L. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0144686 · Cited by 3
Bastonetes Gram-negativos aeróbios e anaeróbios facultativos no fluido ruminal de bovinos de corte alimentados em pastagem lignificada e em novilhos com acidose ruminal
Vieira, E. A., Abrão, F. O., Ribeiro, I. C. O., Nigri, A. C. D. A., da Silva, K. F., Careli, R. T., Geraseev, L. C., & Duarte, E. R. (2015) · Pesquisa Veterinária Brasileira · doi:10.1590/s0100-736x2015000900007 · Cited by 3
In vivo Microbiome Profiling of the Luminal and Mucosal Surface of the Duodenum Using a Cannulated Yearling Bovine Model
Stockler, R. M., Higgins, K. V., Hallowell, H. A., Groover, E. S., Hiltbold, E. M., Newcomer, B. W., & Walz, P. H. (2020) · Frontiers in Veterinary Science · doi:10.3389/fvets.2020.601874 · Cited by 3
Exploring the Role of Fungal Endophytes in the Sudden Death Syndrome of the Invasive Shrub Chrysanthemoides monilifera subsp. rotundata in Australia
Morin, L., Bissett, A. B., & van Klinken, R. D. (2021) · Phytobiomes Journal · doi:10.1094/pbiomes-04-21-0027-r · Cited by 3
Microbial community structure from southern High Plains beef cattle feedyard manure and relationship with nitrous oxide emissions
Waldrip, H. M., Parker, D. B., Miller, S. N., Durso, L. M., Min, B. R., Miller, D. N., Casey, K. D., Woodbury, B. L., & Spiehs, M. J. (2022) · Agrosystems Geosciences & Environment · doi:10.1002/agg2.20292 · Cited by 3
Characterizing the Gut Microbiota of Eurasian Otter (Lutra lutra chinensis) and Snub-Nosed Monkey (Rhinopithecus roxellana) to Enhance Conservation Practices in the Foping National Nature Reserve of China
Zhu, D., Xie, T., Du, R., & Guo, L. J. (2022) · Animals · doi:10.3390/ani12223097 · Cited by 3
“, its diversity) could influence the changes in SCFA quantity and proportion [35].”
Background
Prokaryotic Diversity and Dynamics during Dinoflagellate Bloom Decays in Coastal Tunisian Waters
Lajnef, R., Quéméneur, M., Abdennadher, M., Walha, L. D., Hamza, A., Hassen, M. B., & Zouari, A. B. (2023) · Diversity · doi:10.3390/d15020273 · Cited by 3
“8S-ITS2) regions and the D1–D3 region of the large subunit (LSU) of the ribosomal DNA (28S rDNA) were ampliﬁed using PCR with the primer sets ITS1F/ITS1R [41,42] and D1R/D3ca [43], respectively.”
Effects of dosing non-toxigenic Clostridia on the bacterial populations and immunological responses in the intestinal tract of lactating dairy cows
Kim, H. W., Kim, N. K., Thompson, J., de Jesus, M., Rehberger, J. M., Rehberger, T. G., Smith, A. H., & Mackie, R. I. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1107964 · Cited by 3
Plastic degradation in Lake Geneva: Influence of depth, seasonal shifts, and bacterial community dynamics.
Mori-Bazzano, L., Nguyen, N. H. A., Ševcu, A., Říha, J., Fu, T.-T., Slaveykova, V. I., & Ibelings, B. (2025) · Science of the Total Environment · doi:10.1016/j.scitotenv.2025.179615 · Cited by 2
Gamma radiation in highly compacted FEBEX bentonite: Key microbial and mineralogical behavior for safety assessment of nuclear repositories
Morales‐Hidalgo, M., Povedano‐Priego, C., Martinez-Moreno, M. F., Černá, K., Liskova, K., Říha, J., Valdivieso, P., Alonso, Ú., Fernández, A. M., Jroundi, F., et al. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2025.138915 · Cited by 3
Towards the selection of a produced water enrichment for biological gas hydrate inhibitors
Wilson, S. L., Voordouw, G., & Walker, V. K. (2014) · Environmental Science and Pollution Research · doi:10.1007/s11356-014-2912-x · Cited by 3
“Amplicons were also sequenced (tag-encoded FLX amplicon pyrosequencing) at the RTL using a Roche 454 FLX instrument and titanium reagents using RTL protocols (Dowd et al. 2008).”
Method
Conversion of corn stover hydrolysates to acids: comparison between Clostridium carboxidivorans P7 and microbial communities developed from lake sediment and an anaerobic digester
Xia, C., Kumar, A., Chen, X., Tucker, M. P., & Liang, Y. (2017) · Biomass Conversion and Biorefinery · doi:10.1007/s13399-017-0239-9 · Cited by 3
Animal Gut Microbiomes
Ellis, R. J., & McSweeney, C. S. (2015) · ASM Press eBooks · doi:10.1128/9781555818821.ch4.4.3 · Cited by 4
Acetate Additions Stimulate CO 2 and CH 4 Production from Urban Wetland Soils
Brigham, B. A., Montero, A. D., O'Mullan, G. D., & Bird, J. A. (2018) · Soil Science Society of America Journal · doi:10.2136/sssaj2018.01.0034 · Cited by 3
Common Methods to Understand and Develop Indigenous Probiotics Yeast for Ruminant
Ghazanfar, S., Riaz, A., Ali, G. M., Naveed, S., Arif, I., Irshad, S., Riaz, N., & Manzoor, K. N. (2019) · IntechOpen eBooks · doi:10.5772/intechopen.82731 · Cited by 3
Investigating the effect of biochar on microbial activities and biological processes in soil
Abujabhah, I. S. (2017) · UTAS Research Repository · doi:10.25959/23238881 · Cited by 3
Lactic acid fermentation of human excreta for agricultural application
Andreev, N. (2017) · doi:10.18174/401835 · Cited by 3
Resistant starch inhibits high-fat diet-induced oncogenic responses in the colon of C57BL/6 mice
Zeng, H., Safratowich, B. D., Liu, Z., & Bukowski, M. R. (2025) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2025.109838 · Cited by 4
Florida man exonerated: an amphipod case study on the implications of cryptic species complexes and global invasions
Sawicki, T. R., Cannizzaro, A. G., & Dowd, S. E. (2025) · Biological Invasions · doi:10.1007/s10530-025-03644-y · Cited by 2
“Sequencing was performed at MR DNA (Molecular Research LP; MR DNA, Shallowater, Texas, USA; www. mrdna lab. com ) on a MiSeq following the manufacturer’s guidelines using their universal amplicon sequencing service (bTEFAP(R) (Dowd, et al. 2008), with the primers 18SCrang660F and 18SCrang1025R.”
PPARα deficiency causes skin dysbiosis and triggers innate immunity in keratinocytes
Blunder, S., Minzaghi, D., Pavel, P., Berktold, M., Hermann, M., Ploner, C., Schöpf, C., Marx, F., & Dubrac, S. (2026) · Cell Death and Disease · doi:10.1038/s41419-026-08640-1 · Cited by 2
“Operational taxonomic units (OTUs) were de ﬁ ned after removal of singleton sequences, clustering at 3% divergence (97% similarity) [15 – 18].”
Microbiologically influenced corrosion (MIC) potential of bentonite microorganisms: implications for a deep geological repository for nuclear waste
Černá, K., Mukhtar, S. S., Bureš, R., Alfaro‐Espinoza, G., Koerdt, A., Říha, J., Hlaváčková, V., & Stoulil, J. (2026) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-026-05039-0 · Cited by 2
“For samples with low DNA concentration (< 0.5 ng·µL − 1 ) and high Cq (> 18), a two-step PCR was performed using universal and barcoded fusion primers 515 F (Dowd et al. 2008) and 802R (Claesson et al. 2010) targeting the hypervariable V4 region of the 16 S rRNA gene of both Bacteria and Archaea.”
Influential
Metagenomics of the human microbiome
Shestakov, S. (2011) · Biology Bulletin Reviews · doi:10.1134/s2079086411020095 · Cited by 2
Soil microbiomes from the groundnut basin of Senegal contain plant growth-promoting bacteria with potential for crop improvement in arid soils
Bakhoum, N., Humm, E. A., Khan, N., & Hirsch, A. M. (2024) · Canadian Journal of Microbiology · doi:10.1139/cjm-2024-0031 · Cited by 2
Water Separation and Formation of Cells with Differential Aeration as Factors Controlling Corrosion of Steel Pipelines in a Crude Oil Storage Facility
Šefl, V., Shrestha, R., & Prošek, T. (2024) · Metals · doi:10.3390/met14101098 · Cited by 2
International Symposium on Ruminant Physiology: The holobiont concept in ruminant physiology—More of the same, or something new and meaningful to food quality, food security, and animal health?
Callaway, T. R., Perez, H. G., Corcionivoschi, N., Bu, D., & Fluharty, F. L. (2024) · Journal of Dairy Science · doi:10.3168/jds.2024-25847 · Cited by 3
A preliminary study on farmed and free-ranging mouflons core microbiome
Smoliński, J., Czyż, K., Kleszcz, A., Trusz, A., Wyrostek, A., & Zajfert, K. (2025) · Scientific Reports · doi:10.1038/s41598-025-05443-w · Cited by 2
Coprophilic dipteran community associated with horse dung in Malaysia
Kurahashi, H., Hayashi, T., & Pahang, J. (2015) · Cited by 2
The Influence of the Conditions of the Pet Trade on the Commensal Gastrointestinal Flora of Wild-Caught Tokay Geckos (Gekko gecko)
Casey, C. L., Hernandez, S. M., Yabsley, M. J., Smith, K. F., & Sánchez, S. (2013) · Journal of Herpetological Medicine and Surgery · doi:10.5818/1529-9651-23.3.74 · Cited by 2
COMMUNITY ANALYSIS OF A UNIQUE FULL-SCALE WASTEWATER TREATMENT PLANT AS REVEALED BY 454-PYROSEQUENCING
Preut, M. C. (2014) · UNM’s Digital Repository (University of New Mexico) · Cited by 2
Changes in the rumen bacterial microbiome of cattle exposed to ponderosa pine needles
Welch, K. D., Stonecipher, C. A., Gardner, D. R., Cook, D., & Pfister, J. A. (2017) · Journal of Animal Science · doi:10.2527/jas.2016.1228 · Cited by 2
Cattle Gastrointestinal Tract Microbiota in Health and Disease
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Molecular techniques for understanding microbial abundance and activity in clay barriers used for geodisposal
Mijnendonckx, K., Monsieurs, P., Černá, K., Hlaváčková, V., Steinová, J., Burzan, N., Bernier‐Latmani, R., Boothman, C., Miettinen, H., Kluge, S., et al. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-818695-4.00004-6 · Cited by 2
Potential for Passive Treatment of Coal Mine-derived Acid Mine Drainage in Abandoned Stream Channels
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Pesciaroli, C., Purswani, J., Mestelan, S. A., Lett, L., Portela, G., Médici, S., Morillo, J. A., Pozo, C., González-López, J., & Rivadeneyra, M. A. (2021) · Geomicrobiology Journal · doi:10.1080/01490451.2021.1968980 · Cited by 2
Was the decline of saltmarsh tabanid populations after the 2010 oil spill associated with change in the larval food web?
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New Pond—Indicator Bacteria to Complement Routine Monitoring in a Wet/Dry Tropical Wastewater Stabilization System
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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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