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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MethodInfluential
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“[98] Dowd S E, Callaway T R, Wolcott R D, Sun Y, McKeehan T, Hagevoort R G, Edrington T S.”
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Padovan, A. C., Neave, M. J., Munksgaard, N. C., & Gibb, K. S. (2017) · Environmental Monitoring and Assessment · doi:10.1007/s10661-017-5842-5 · Cited by 8
Photoreactivity of riverine and phytoplanktonic dissolved organic matter and its effects on the dynamics of a bacterial community from the coastal Mediterranean Sea
Blanchet, M., Fernández, C., & Joux, F. (2017) · Progress In Oceanography · doi:10.1016/j.pocean.2017.03.003 · Cited by 8
“8 GWATTACCGCGGCKGCTG-3) as described previously (Dowd et al. 2008).”
Method
Applied Injected Air into Subsurface Drip Irrigation: Plant Uptake of Pharmaceuticals and Soil Microbial Communities
D’Alessio, M., Durso, L. M., Williams, C. F., Olson, C. A., Ray, C., & Paparozzi, E. T. (2019) · Journal of Environmental Engineering · doi:10.1061/(asce)ee.1943-7870.0001655 · Cited by 8
“The DNA was eluted in 100 μL and used as a template for amplicon pyrosequencing analysis, which was performed by MR DNA Laboratory (Shallow Water, TX) using universal eubacterial primers 515F and 806R in a single-step PCR, followed by Ion Torrent PGM sequencing (Dowd et al. 2008).”
Method
Comparison of Microbial Communities Isolated from Feces of Asymptomatic Salmonella-Shedding and Non-Salmonella Shedding Dairy Cows
Haley, B. J., Pettengill, J., Gorham, S., Ottesen, A., Karns, J. S., & Kessel, J. A. S. V. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00691 · Cited by 9
Diversity of Microbiomes in Beef Cattle
Durso, L. M., Wells, J. E., & Kim, M. S. (2014) · Springer eBooks · doi:10.1007/978-1-4614-6418-1_730-4 · Cited by 8
Characterization of the ruminal microbiota in sheep and goats fed different levels of tannin-rich Sericea lespedeza hay
Min, B. R., Wang, W. L., Pitta, D., Indugu, N., Patra, A. K., Wang, H. H., Abrahamsen, F. W., Hilaire, M., & Puchała, R. (2024) · Journal of Animal Science · doi:10.1093/jas/skae198 · Cited by 10
Fermented total mixed ration enhances nutrient digestibility and modulates the milk components and fecal microbial community in lactating Holstein dairy cows
Wang, L., Jin, S., Wang, P., Li, X., Liu, C., Sun, S., Zhang, G., Chang, J., Yin, Q., Zhang, H., et al. (2024) · Frontiers in Veterinary Science · doi:10.3389/fvets.2024.1408348 · Cited by 11
Glucose Metabolism-Modifying Natural Materials for Potential Feed Additive Development
Lin, W. C., Hoe, B. C., Li, X., Lian, D., & Zeng, X. (2024) · Pharmaceutics · doi:10.3390/pharmaceutics16091208 · Cited by 7
“Interestingly, raffinose, usually seen as an anti-nutritional compound, enhanced GLUT4 translocation via phosphorylation of IR β /PI3K/Akt in differentiated L6 myocytes and 3T3-L1 preadipocytes [173].”
Background
Comparative Analysis of Microbiota in Jiani Yaks with Different Rib Structures
Cidan, Y., Lü, S., Wang, H., Wang, J., Ali, M., Fouad, D., Ataya, F. S., Zhu, Y., Basang, W., & Li, K. (2024) · Life · doi:10.3390/life14111458 · Cited by 7
Soil Microbial Responses to Varying Environmental Conditions in a Copper Belt Region of Africa: Phytoremediation Perspectives
Nkongolo, K. K. C., Mukalay, J. B., Lubobo, A. K., & Michael, P. (2024) · Microorganisms · doi:10.3390/microorganisms13010031 · Cited by 7
Cohabitation with farm animals rather than breeding effort increases the infection with feather‐associated bacteria in the barn swallow Hirundo rustica
Fülöp, A., Vágási, C. I., & Pap, P. L. (2017) · Journal of Avian Biology · doi:10.1111/jav.01262 · Cited by 7
Rhizosphere Diazotrophs and Other Bacteria Associated with Native and Encroaching Legumes in the Succulent Karoo Biome in South Africa
Muema, E. K., Steenkamp, E. T., & Venter, S. N. (2022) · Microorganisms · doi:10.3390/microorganisms10020216 · Cited by 7
Epibiotic bacteria on the carapace of hawksbill and green sea turtles
Loghmannia, J., Nasrolahi, A., & Dobretsov, S. (2023) · Biofouling · doi:10.1080/08927014.2023.2220275 · Cited by 7
“First, PCR was performed with the bacterial hypervariable regions V3–V4 of the 16S rRNA genes using forward primer 515 F (50-GTGCCAGCMGCCGCGG TAA-30) and reverse primer 806R (50-GGGACTAC HVGGTWTCTAAT-30) (Dowd et al. 2008).”
BackgroundMethod
Bacterial diversity within five unexplored freshwater lakes interconnected by surface channels in East Antarctic Dronning Maud Land (Schirmacher Oasis) using amplicon pyrosequencing
Huang, J. P., Swain, A. K., Andersen, D. T., & Bej, A. K. (2014) · Polar Biology · doi:10.1007/s00300-013-1436-z · Cited by 7
“The initial generation of the genomic library was performed by utilizing a one-step PCR with a total of 30 cycles of amplification (Dowd et al. 2008), using the oligonucleotide primers 341F (50–CCT ACG GGA GGC AGC AG–30 (Muyzer et al. 1993) and 907R (50–CCG TCA ATT CMT TTG AGT TT–30 (Lane et al.…”
MethodInfluential
Characterization of bacterium types isolated from commercial laying hen farms in Ogun State Nigeria
Adebowale, O. O., & Adeyemo, O. K. (2018) · Revue d’élevage et de médecine vétérinaire des pays tropicaux · doi:10.19182/remvt.31642 · Cited by 7
“Apart from consequences on poultry production, many other species belonging to Enterobacteriaceae or non-Enterobacteriaceae have been implicated as opportunistic, nosocomial and foodborne pathogens responsible for a wide range of infections in humans, especially in critically ill or immunocompromised patients (Dowd et…”
Background
Evaluating the Effects of Pine and Miscanthus Biochar on Escherichia coli, Total Aerobic Bacteria, and Bacterial Communities in Commercial Broiler Litter
Mohammadi-Aragh, M. K., Linhoss, J. E., Marty, C. A., Evans, J. D., PURSWELL, J. L., Chaves-Córdoba, B., Chesser, G. D., & Lowe, J. W. (2022) · Avian Diseases · doi:10.1637/aviandiseases-d-22-00056 · Cited by 7
“Bacterial communities were analyzed on the Illumina NovaSeq platform via the bTEFAPt (MRDNA, Shallowater, TX) DNA analysis service, which has been previously used to successfully characterize microbiomes from various environments (36,37,38,39).”
Method
Indoor Bacterial and Fungal Burden in “Moldy” versus “Non-Moldy” Homes: A Case Study Employing Advanced Sequencing Techniques in a US Metropolitan Area
Chauhan, B. V., Jones, D. H., Banerjee, G., Agrawal, S., Sulaiman, I. M., Jia, C., & Banerjee, P. (2023) · Pathogens · doi:10.3390/pathogens12081006 · Cited by 7
“The final fasta file containing the cleaned sequences was used to construct the Operational Taxonomic Units (OTUs) following the MR DNA analysis pipeline (MR DNA, Shallowater, TX, USA) [33] for the downstream analysis of the bacterial and fungal composition.”
Method
Genomics of Probiotic–Host Interactions
Ajithdoss, D. K., Dowd, S. E., & Suchodolski, J. S. (2011) · Springer eBooks · doi:10.1007/978-1-4614-1311-0_4 · Cited by 7
Surface modification of an organic hessian substrate leads to shifts in bacterial biofilm community composition and abundance
Paterson, J. S., Ogden, S., Smith, R. J., Delpin, M. W., Mitchell, J. G., & Quinton, J. S. (2015) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2015.12.033 · Cited by 7
Efficient agglomerative hierarchical clustering for biological sequence analysis
Nguyen, T.-D., & Kwoh, C.-K. (2015) · IEEE Region 10 Conference (TENCON) · doi:10.1109/tencon.2015.7373194 · Cited by 7
“5× 10(5) reads 4742 OTUs in the hands 230bp of 51 people Human wound [9] 2.”
Background
Microbial community structure of Arctic seawater as revealed by pyrosequencing
Li, Y., Wang, Z., & Lin, X. (2016) · Acta Oceanologica Sinica · doi:10.1007/s13131-015-0742-4 · Cited by 7
Microbial diversity and distribution differ between water column and biofilm assemblages in arid-land waterbodies
Kaestli, M., Munksgaard, N. C., Gibb, K. S., & Davis, J. A. (2019) · Freshwater Science · doi:10.1086/706106 · Cited by 7
Levels of Main Bacterial Phyla in the Gastrointestinal Tract of Sheep Depending on Parity and Age
Smoliński, J., Szeligowska, N., Cholewińska, P., Czyż, K., & Janczak, M. (2021) · Animals · doi:10.3390/ani11082203 · Cited by 7
“Universal Eubacterial Genes [13] 530F (5′-GTC CCA GCM GCN GCG G) 1100R (5′-GGG TTN CGN TCG TTG) Firmicutes [14] 928F-Firm (5′-TGA AAC TYA AAG GAA TTG ACG) 1040FirmR (5′-ACC ATG CAC CAC CTG TC) Bacteroidetes [14] 798cfbF (5′-CRA ACA GGA TTA GAT ACC CT) cfb967R (5′-GGT AAG GGT TCC TCG CGT AT) Proteobacteria [15] 27F (5′…”
Background
Variation in archaeal and bacterial community profiles and their functional metabolic predictions under the influence of pure and mixed fertilizers in paddy soil
Barq, M. G., Hassan, M. M., Yasmin, H., Shahzad, A., Malik, N. H., Lorenz, N., Alsahli, A. A., Dick, R. P., & Ali, N. (2021) · Saudi Journal of Biological Sciences · doi:10.1016/j.sjbs.2021.08.091 · Cited by 7
Population Genetics and Microbial Communities of the Gopher Tortoise ( Gopherus polyphemus )
Gaillard, D. L. (2014) · Cited by 7
A METAGENOMIC STUDY OF THE TICK MIDGUT
Yuan, D. T. (2010) · Digital Commons-TMC (Texas Medical Center) · Cited by 7
Methylmercury Production in Riverbank Sediments of the South River, Virginia (USA) and Assessment of Biochar as a Mercury Treatment Option
Paulson, K. M. A. (2014) · UWSpace (University of Waterloo) · Cited by 7
Comparative analysis of gut microbiota in free range and house fed yaks from Linzhou County
Wang, H., Ali, M., Zhu, Y., Chen, X., Lu, D., Liu, Y., Li, K., & Zhang, C. (2025) · Scientific Reports · doi:10.1038/s41598-025-95357-4 · Cited by 6
“It is possible that the enhancement of Firmicutes and Bacteroides in the LS group was to efficiently decompose lignin and cellulose and non-fibrous compounds 34,35 .”
Microbial diversity at remediated former gold and copper mines and the metal tolerance of indigenous microbial strains
Velianyk, V., Palušák, M., Nguyen, N. H. A., Říha, J., Ševců, A., Černík, M., & Hlaváčková, V. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.02555-24 · Cited by 6
Effect of olive cake supplementation on faecal microbiota profile of Holstein and Modicana dairy cattle
Floridia, V., Russo, N., D’Alessandro, E., Lopreiato, V., Pino, A., Amato, A., Liotta, L., Caggia, C., & Randazzo, C. L. (2023) · Microbiological Research · doi:10.1016/j.micres.2023.127510 · Cited by 6
Comparative analysis of intestinal microbiota composition between free-ranged captive yak populations in Nimu County
Zhu, Y., Lü, S., Cidan, Y., Wang, H., Li, K., & Basang, W. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1420389 · Cited by 6
Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties
Ferrando, L., Rariz, G., Martínez-Pereyra, A., & Scavino, A. F. (2024) · Journal of Applied Microbiology · doi:10.1093/jambio/lxae157 · Cited by 6
Bentonite sterilization methods in relation to geological disposal of radioactive waste: comparative efficiency of dry heat and gamma radiation
Bartak, D., Říha, J., Dudáš, D., Gallus, P., Bedrníková, E., Kašpar, V., & Černá, K. (2025) · Journal of Applied Microbiology · doi:10.1093/jambio/lxaf051 · Cited by 6
Amplicon pyrosequencing of wild duck eubacterial microbiome from a fecal sample reveals numerous species linked to human and animal diseases
Strong, T., Dowd, S. E., Gutierrez, A. F., & Coffman, J. (2013) · F1000Research · doi:10.12688/f1000research.2-224.v1 · Cited by 6
“Methods Amplicon pyrosequencing (bTEFAP) was originally described by Dowd et al.10 and has been used in describing a wide range of environmental and health related microbiomes including the intestinal populations of a variety of animals and their environments including cattle11–15.”
Method
Microbial and Physicochemical Status of Raw and Processed Sea Cucumbers from the Hellenic Seawaters
Boziaris, I. S., Anagnostopoulos, D. A., Parlapani, F. F., Syropoulou, F., Martsikalis, P. V., Apostologamvrou, C., Kokioumi, D., & Vafidis, D. (2023) · Sustainability · doi:10.3390/su151813467 · Cited by 6
Bacterial community assessment of drinking water and downstream distribution systems in highland localities of Ecuador
Molina, C. A., Quiroz-Moreno, C. D., Jarrín–V, P., Díaz, M., Yugsi, E., Pérez, J., & Baldeón, L. (2024) · Journal of Water and Health · doi:10.2166/wh.2024.290 · Cited by 9
Microenvironment and phylogenetic diversity of P rochloron inhabiting the surface of crustose didemnid ascidians
Nielsen, D. A., Pernice, M., Schliep, M., Sablok, G., Jeffries, T. C., Kühl, M., Wangpraseurt, D., Ralph, P. J., & Larkum, A. W. D. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.12983 · Cited by 6
Amplicon pyrosequencing and ion torrent sequencing of wild duck eubacterial microbiome from fecal samples reveals numerous species linked to human and animal diseases
Strong, T., Dowd, S. E., Gutierrez, A. F., Molnár, D., & Coffman, J. A. (2013) · F1000Research · doi:10.12688/f1000research.2-224.v2 · Cited by 6
“Methods Amplicon pyrosequencing (bTEFAP) was originally described by Dowd et al.10 and has been used in describing a wide range of environmental and health related microbiomes including the intestinal populations of a variety of animals and their environments including cattle11–15.”
Method
Comparison of bacterial diversity in large intestine of Xiangxi yellow cattle (Bos taurus) associated with different diet: Fresh Miscanthus sinensis and mixed forage
Li, Y. (2012) · African Journal of Microbiology Research · doi:10.5897/ajmr12.616 · Cited by 6
“Lachnospiraceae bacterium has been reported as a ubiquitous and important bacteria which could be often detected in the digestive tract of cattle (Dowd et al., 2008).”
BackgroundMethod
454 Pyrosequencing and Direct Plating Reveal high Fungal Diversity and Dominance by Saprophytic Species in Organic Compost
Al-Mazroui, S. S., & Al-Sadi, A. M. (2015) · International Journal of Agriculture and Biology · doi:10.17957/ijab/15.0068 · Cited by 6
“Pyrosequencing was carried out based on the 18S rRNA as described by Dowd et al. (2008a, 2008b).”
Method
Characterization and Investigation of Fungi Inhabiting the Gastrointestinal Tract of Healthy and Diseased Humans
Haute, M. J. S. V. (2015) · Lincoln (University of Nebraska) · Cited by 6
Can inoculation with living soil standardize microbial communities in soilless potting substrates?
Bukovská, P., Püschel, D., Hršelová, H., Jansa, J., & Gryndler, M. (2016) · Applied Soil Ecology · doi:10.1016/j.apsoil.2016.09.005 · Cited by 6
Metagenomic analysis of enteric bacterial pathogens affecting the performance of dairy cows in smallholder productions systems
Habimana, V., Bett, R. C., Joshua, O. A., Felix, M. K., Githae, D., & Joseph, O. (2018) · African Journal of Microbiology Research · doi:10.5897/ajmr2018.8849 · Cited by 4
“Additionally, the use of next generation sequencing (NGS) techniques, bioinformatic tools, and molecular based approaches is the potential laboratory way for studying the diversity of rumen microbiota of health individuals (Dowd et al., 2008).”
Background
Soil bacterial community associated with the dioecious Acanthosicyos horridus in the Namib Desert
Unc, A., Maggs‐Kölling, G., Marais, E., Sherman, C., Doniger, T., & Steinberger, Y. (2019) · Biology and Fertility of Soils · doi:10.1007/s00374-019-01358-7 · Cited by 6
“The reaction mix used for both PCR runs consisted of 5 μl 5X Phusion®HF reaction buffer, 0.5 μl of 10 mM dNTPs mix, 1 μl of 1 mM forward primer, 1 μl of 1 mM reverse primer, 0.25 μl Phusion® HFDNA polymerase (2 U/μl), and 1μl extracted DNA for each sample (Dowd et al. 2008).”
MethodInfluential
Ciprofloxacin Prophylaxis in Emergency Response Plans Would Alter Bacterial Communities in Wastewater Treatment Infrastructure
Fu, X., Johnson, W. L., Gustafson, J. E., Wang, Y., Wang, X., Chitica, I., Lanier, B. M., Deng, S., & Krzmarzick, M. J. (2021) · Environmental Engineering Science · doi:10.1089/ees.2020.0316 · Cited by 6
“…polymerase chain reaction ampliﬁcation of the V4 variable region of 16S rRNA genes with primers 515F (5 0 -GTGCCAGCMGCC GCGGTAA-3 0 ) and 806R (5 0 -GGACTACVSGGGTATCT AAT-3 0 ) (Caporaso et al. , 2012) and bTEFAP (cid:2) Illumina MiSeq 2 · 300 bp barcoded amplicon sequencing (Dowd et al. , 2008).”
Levels of Firmicutes, Actinobacteria Phyla and Lactobacillaceae Family on the Skin Surface of Broiler Chickens (Ross 308) Depending on the Nutritional Supplement and the Housing Conditions
Cholewińska, P., Michalak, M., Wojnarowski, K., Skowera, S., Smoliński, J., & Czyż, K. (2021) · Agriculture · doi:10.3390/agriculture11040287 · Cited by 7
“Universal Eubacterial genes 530F (5′-GTC CCA GCM GCN GCG G) 1100R (5′-GGG TTN CGN TCG TTG) [12]”
Background
Sulfur Cycling as a Viable Metabolism under Simulated Noachian/Hesperian Chemistries
Oliver, J. A. W., Kelbrick, M., Ramkissoon, N. K., Dugdale, A., Stephens, B. P., Kucukkilic-Stephens, E., Fox‐Powell, M. G., Schwenzer, S. P., Antunes, A., & Macey, M. C. (2022) · Life · doi:10.3390/life12040523 · Cited by 6
“The data were processed by Mr DNA using a customized pipeline [25,26].”
Method

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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