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

The DOI matches its Crossref record; 82 of the 82 references it cites were found in a registry or an index.

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

Open access

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

Open this paper in CoChat — free account Open PDF

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1186/1471-2180-8-125

Cites

82 of 82 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · cited 2×
“The resulting TC FASTA for each sample was then evaluated using BLASTn [77] against a custom database derived from the RDP-II database [78] and GenBank http://ncbi.”
Method
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444 · cited 1×
“Results and Discussion Recent research related to host physiology (obesity) and the gastrointestinal bacterial populations have sparked a renewed interest in understanding the gut microbiome [26,27].”
Background
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785 · cited 1×
“Results and Discussion Recent research related to host physiology (obesity) and the gastrointestinal bacterial populations have sparked a renewed interest in understanding the gut microbiome [26,27].”
Background
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913 · cited 1×
“Information on microbial diversity within the gastrointestinal tract of humans has increased in recent years as a result of 16S rDNA-based analyses [9,10], yet similar data on the microbiomes of livestock is lacking [11,12].”
Background
Food-Related Illness and Death in the United States
Mead, P. S., Slutsker, L., DIETZ, V. J., McCaig, L. F., Bresee, J., Shapiro, C. A., Griffin, P. M., & Tauxe, R. V. (1999) · Emerging infectious diseases · doi:10.3201/eid0505.990502 · Cited by 7,305
CAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261 · cited 3×
“The ace files generated by CAP3 were then processed to generate a secondary FASTA file containing the tentative consensus (TC) sequences of the assembly along with the number of reads integrated into each consensus.”
MethodInfluential
Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine
Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.02.017 · Cited by 3,358 · cited 1×
“Information on microbial diversity within the gastrointestinal tract of humans has increased in recent years as a result of 16S rDNA-based analyses [9,10], yet similar data on the microbiomes of livestock is lacking [11,12].”
Background
The Rumen and Its Microbes
Hungate, R. E. (2013) · Elsevier eBooks · doi:10.1016/c2013-0-12555-x · Cited by 3,060
Bacteroides : the Good, the Bad, and the Nitty-Gritty
Wexler, H. M. (2007) · Clinical Microbiology Reviews · doi:10.1128/cmr.00008-07 · Cited by 2,388
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis
von Wintzingerode, F., Göbel, U. B., & Stackebrandt, E. S. (1997) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.1997.tb00351.x · Cited by 2,085

Show all 80 references

Sorted by citations

Items 501–600 of 1,000

Alterations in Ileal Mucosa Bacteria Related to Diet Complexity and Growth Performance in Young Pigs
Levesque, C. L., Hooda, S., Swanson, K. S., & de Lange, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0108472 · Cited by 34
High throughput sequencing methods for microbiome profiling: application to food animal systems
Highlander, S. K. (2012) · Animal Health Research Reviews · doi:10.1017/s1466252312000126 · Cited by 34
“Holstein cow Feces Survey of commensals and potential food-borne pathogens in 20 animals 454 FLX V4–V5 rDNA amplicons (Dowd et al., 2008)”
BackgroundMethodInfluential
Re-assessment of phenotypic identifications of Bacteroides putredinis to Alistipes species using molecular methods
Tyrrell, K. L., Warren, Y. A., Citron, D. M., & Goldstein, E. J. C. (2011) · Anaerobe · doi:10.1016/j.anaerobe.2011.04.002 · Cited by 33
“Typically,Alistipes are found in mixed cultures [3,4] and to date have been found also in non-human intestinal microbiomes including cattle and turkeys [7,8].”
Background
Evaluation of in vitro gas production and rumen bacterial populations fermenting corn milling (co)products
Williams, W. L., Tedeschi, L. O., Kononoff, P. J., Callaway, T. R., Dowd, S. E., Karges, K. K., & Gibson, M. L. (2010) · Journal of Dairy Science · doi:10.3168/jds.2009-2920 · Cited by 33
“One of the newest methods to identify bacteria utilizes DNA pyrosequencing, which characterizes bacterial populations on a phylogenetic basis (Dowd et al., 2008a,b,c).”
Influential
Utilizing pyrosequencing and quantitative PCR to characterize fungal populations among house dust samples
Nonnenmann, M. W., Coronado, G. D., Thompson, B., Griffith, W. C., Hanson, J. D., Vesper, S. J., & Faustman, E. M. (2012) · Journal of Environmental Monitoring · doi:10.1039/c2em30229b · Cited by 33
Endosymbiotic Candidates for Parasitoid Defense in Exotic and Native New Zealand Weevils
White, J. A., Richards, N. K., Laugraud, A., Saeed, A., Curry, M. M., & McNeill, M. R. (2015) · Microbial Ecology · doi:10.1007/s00248-014-0561-8 · Cited by 33
Microbial Communities Promoting Mn(II) Oxidation in Ashumet Pond, a Historically Polluted Freshwater Pond Undergoing Remediation
Santelli, C. M., Chaput, D. L., & Hansel, C. M. (2014) · Geomicrobiology Journal · doi:10.1080/01490451.2013.875605 · Cited by 35
“Bacterial 16S rRNA gene tag-encoded FLX amplicon pyrosequencing (bTEFAP) was carried out directly from the environmental DNA as described by Dowd et al. (2008).”
Method
Gut microbial communities associated with the molting stages of the giant freshwater prawn Macrobrachium rosenbergii
Mente, E., Gannon, A. T., Nikouli, E., Hammer, H. S., & Kormas, K. A. (2016) · Aquaculture · doi:10.1016/j.aquaculture.2016.05.045 · Cited by 33
Effect of high sulfate concentrations on chalcopyrite bioleaching and molecular characterisation of the bioleaching microbial community
Boxall, N. J., Rea, S. M., Li, J., Morris, C. J., & Kaksonen, A. H. (2016) · Hydrometallurgy · doi:10.1016/j.hydromet.2016.07.006 · Cited by 33
Changes in bacterial community composition of Escherichia coli O157:H7 super-shedder cattle occur in the lower intestine
Zaheer, R., Dugat‐Bony, É., Holman, D. B., Cousteix, E., Xu, Y., Munns, K. D., Selinger, L. J., Barbieri, R., Alexander, T. W., McAllister, T. A., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0170050 · Cited by 33
“However, this genus is also ubiquitous and relatively abundant within the rumen and lower GI tract of healthy cattle as evidenced from previous microbiome studies [22, 26, 46, 53].”
Background
Ecological patterns in the skin microbiota of frogs from tropical Australia
Christian, K. A., Weitzman, C. L., Rose, A. M., Kaestli, M., & Gibb, K. S. (2018) · Ecology and Evolution · doi:10.1002/ece3.4518 · Cited by 33
Impacts of a glyphosate-based herbicide on the gut microbiome of three earthworm species (Alma millsoni, Eudrilus eugeniae and Libyodrilus violaceus): A pilot study
Owagboriaye, F. O., Mesnage, R., Dedeke, G. A., Adegboyega, T., Aladesida, A. A., Adeleke, M. T., Owa, S. O., & Antoniou, M. N. (2021) · Toxicology Reports · doi:10.1016/j.toxrep.2021.03.021 · Cited by 33
“singleton sequencesand clustering at 3% divergence (97 % similarity) [30].”
BackgroundMethod
MEAT SCIENCE AND MUSCLE BIOLOGY SYMPOSIUM:Escherichia coli O157:H7, diet, and fecal microbiome in beef cattle12
Wells, J. E., Kim, M., Bono, J. L., Kuehn, L. A., & Benson, A. K. (2014) · Journal of Animal Science · doi:10.2527/jas.2013-7282 · Cited by 33
Design Defines the Effects of Nanoceria at a Low Dose on Soil Microbiota and the Potentiation of Impacts by the Canola Plant
Hamidat, M., Barakat, M., Ortet, P., Chanéac, C., Rose, J., Bottero, J., Heulin, T., Achouak, W., & Santaella, C. (2016) · Environmental Science & Technology · doi:10.1021/acs.est.6b01056 · Cited by 33
Successional biocrust stages on dead shrub soil mounds after severe drought: Effect of micro-geomorphology on microbial community structure and ecosystem recovery
Nejidat, A., Potrafka, R. M., & Zaady, E. (2016) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2016.08.028 · Cited by 33
Regime Shift in Sandy Beach Microbial Communities following Deepwater Horizon Oil Spill Remediation Efforts
Engel, A. S., & Gupta, A. A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0102934 · Cited by 32
“Aliquots of triplicate DNA extractions for each of the samples were homogenized and purified for pyrosequencing of the V1–V3 hypervariable region of the 16S rRNA genes, with the forward primer 28F (59TTTGATCNTGGCTCAG-39) and reverse primer 519r (59GTNTTACNGCGGCKGCTG-39), using GS FLX Titanium technology (Roche 454 Lif…”
Method
Identification And Location Of Symbionts Associated With Potato Psyllid (Bactericera cockerelli) Lifestages
Hail, D., Dowd, S. E., & Bextine, B. R. (2012) · Environmental Entomology · doi:10.1603/en11198 · Cited by 32
Effect of Dietary Supplementation of Moringa Oleifera on the Production Performance and Fecal Methanogenic Community of Lactating Dairy Cows
Dong, L., Zhang, T., & Diao, Q. (2019) · Animals · doi:10.3390/ani9050262 · Cited by 39
The effect of low-pH concrete on microbial community development in bentonite suspensions as a model for microbial activity prediction in future nuclear waste repository
Shrestha, R., Černá, K., Špánek, R., Bartak, D., Černoušek, T., & Ševců, A. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.151861 · Cited by 32
Rhizosphere microbiome selection by Epichloë endophytes of Festuca arundinacea
Roberts, E. L., & Ferraro, A. R. (2015) · Plant and Soil · doi:10.1007/s11104-015-2585-3 · Cited by 32
“Operational taxonomic units were defined after removal of singleton sequences, and clustering at 3 % divergence (97 % similarity) (Dowd et al. 2008; Dowd et al. 2008; Edgar 2010; Capone et al. 2011; Eren et al. 2011; Swanson et al. 2011).”
Method
An assessment of microbial communities associated with surface mining-disturbed overburden
Poncelet, D. M., Cavender, N. D., Cutright, T. J., & Senko, J. M. (2013) · Environmental Monitoring and Assessment · doi:10.1007/s10661-013-3505-8 · Cited by 32
“Partial sequences of bacterial 16S rRNA genes were obtained using tag-encoded FLX amplicon pyrosequencing at Research and Testing Laboratories (Lubbock, TX) using Gray28f (5 ′-TTTGATCNTGGCTCAG-3 ′) and Gray519r (5′GTNTTACNGCGGCKGCTG-3′) primers (Dowd et al. 2008).”
Method
Effect of dietary crude protein modification on ammonia and nitrous oxide concentration on a tie-stall dairy barn floor
Arriaga, H., Díaz, G. S., Martínez-Suller, L., Calsamiglia, S., & Merino, P. (2010) · Journal of Dairy Science · doi:10.3168/jds.2009-2906 · Cited by 32
Phylogenetic Analysis and Metabolic Potential of Microbial Communities in an Industrial Bagasse Collection Site
Kanokratana, P., Mhuantong, W., Laothanachareon, T., Tangphatsornruang, S., Eurwilaichitr, L., Pootanakit, K., & Champreda, V. (2013) · Microbial Ecology · doi:10.1007/s00248-013-0209-0 · Cited by 32
“Recently, tagged amplicon pyrosequencing or bacterial tag encoded FLX amplicon pyrosequencing has been introduced for highthroughput sequencing of specific target genes, in particular the 16S rRNA gene as a marker for biodiversity [5].”
Background
Alternating or continuous exposure to cafeteria diet leads to similar shifts in gut microbiota compared to chow diet
Kaakoush, N. O., Martire, S. I., Raipuria, M., Mitchell, H. M., Nielsen, S. J., Westbrook, R. F., & Morris, M. J. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201500815 · Cited by 32
“The composition of the microbial communities was assessed by high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene using Tag-encoded FLX amplicon pyrosequencing (28F, average read length: 400 bp, region: V1-3) based upon established and validated protocols [21].”
Effectiveness of Devices to Monitor Biofouling and Metals Deposition on Plumbing Materials Exposed to a Full-Scale Drinking Water Distribution System
Ginige, M. P., Garbin, S., Wylie, J. T., & Krishna, K. C. B. (2017) · PLoS ONE · doi:10.1371/journal.pone.0169140 · Cited by 32
Variation of Oxygenation Conditions on a Hydrocarbonoclastic Microbial Community Reveals Alcanivorax and Cycloclasticus Ecotypes
Terrisse, F., Cravo‐Laureau, C., Noël, C., Cagnon, C., Dumbrell, A. J., McGenity, T. J., & Duran, R. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01549 · Cited by 32
“Amplicon 454-pyrosequencing was performed by the Molecular Research DNA laboratory (MR DNA, Shallowater, TX, United States) following process originally described by Dowd et al. (2008).”
Method
Core vs. diet -associated and postprandial bacterial communities of the rainbow trout (Oncorhynchus mykiss) midgut and feaces
Mente, E., Nikouli, E., Antonopoulou, E., Martín, S., & Kormas, K. A. (2018) · Biology Open · doi:10.1242/bio.034397 · Cited by 38
“…(Martínez-Porchas et al., 2016) of the 16S rRNA gene by using the primer pair S-DBact-0341-b-S-17 (5′-CCTACGGGNGGCWGCAG-3′) and S-DBact-0785-a-A-21 (5′-GACTACHVGGGTATCTAATCC-3′) (Klindworth et al., 2012) according to Dowd et al. (2008) at the MRDNA Ltd. (Shallowater, TX, USA) sequencing facilities.”
Method
Enrichment of anodophilic nitrogen fixing bacteria in a bioelectrochemical system
Wong, P. Y., Cheng, K. Y., Kaksonen, A. H., Sutton, D. C., & Ginige, M. P. (2014) · Water Research · doi:10.1016/j.watres.2014.06.046 · Cited by 31
“The method used for the 454 pyrosequencing was described by Dowd et al. (2008).”
Method
A Global Comparison ofBactericera cockerelli(Hemiptera: Triozidae) Microbial Communities
Arp, A. P., Munyaneza, J. E., Crosslin, J. M., Trumble, J. T., & Bextine, B. R. (2014) · Environmental Entomology · doi:10.1603/en13256 · Cited by 31
“Primers used for pyrosequencing were Gray28F 5 TTT GAT CNT GGC TCA G 3 and Gray519R 5 GTN TTA CNG CGG CKG CTG 3 (Dowd et al. 2008; Hail et al. 2010, 2011).”
Method
Cultivated and fallow fields harbor distinct communities of Basidiomycota
Kjøller, R., & Rosendahl, S. (2014) · Fungal ecology · doi:10.1016/j.funeco.2014.02.005 · Cited by 31
Analysis of biodegradation by-products of nitrobenzene and aniline mixture by a cold-tolerant microbial consortium
Na, L., Li, H., Ding, F., Xiu, Z., Liu, P., & Yu, Y. (2013) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2013.05.033 · Cited by 31
Microbial Diversity of Source and Point-of-Use Water in Rural Haiti – A Pyrosequencing-Based Metagenomic Survey
Mukherjee, N., Bartelli, D., Patra, C., Chauhan, B. V., Dowd, S. E., & Banerjee, P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0167353 · Cited by 32
Association between animal age and the prevalence of Shiga toxin-producing Escherichia coli in a cohort of beef cattle
Mir, R. A., Weppelmann, T. A., Kang, M., Bliss, T. M., DiLorenzo, N., Lamb, G. C., Ahn, S., & Jeong, K. C. (2014) · Veterinary Microbiology · doi:10.1016/j.vetmic.2014.12.016 · Cited by 30
“It has been reported that increased microbial diversity may inhibit pathogen proliferation and can lead to lower rates of colonization in animals (Dowd et al., 2008; Durso et al., 2010; Zhao et al., 2013) and persistence in manure (Kim and Jiang, 2010; Kim et al., 2009).”
Background
454-Pyrosequencing Reveals Variable Fungal Diversity Across Farming Systems
Kazerooni, E. A., & Al-Sadi, A. M. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.00314 · Cited by 30
“The resulting sequences were analyzed using a BLASTn.NET algorithm by comparison to high quality sequences from NCBI and the outputs were validated based on taxonomic distance methods (Dowd et al., 2005, 2008a,b).”
MethodInfluential
Lactobacilli Are Prominent Members of the Microbiota Involved in the Ruminal Digestion of Barley and Corn
Yang, H. E., Zotti, C. A., McKinnon, J. J., & McAllister, T. A. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00718 · Cited by 29
“The 16S rRNA gene universal bacterial primers 27F-519R (27F 5’-AGRGTTTGATCMTGGCTCAG, 519R 5’- GTNTTACNGCGGCKGCTG), were used to amplify the hypervariable regions V1 to V3 of the 16S rRNA gene as described by Dowd et al. (2008).”
Method
Syntroph diversity and abundance in anaerobic digestion revealed through a comparative core microbiome approach
Fujimoto, M., Carey, D. E., Zitomer, D., & McNamara, P. J. (2019) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-019-09862-4 · Cited by 30
Unravelling plasmidome distribution and interaction with its hosting microbiome
Kav, A. B., Rozov, R., Bogumil, D. D., Sørensen, S. J., Hansen, L. H., Benhar, I., Halperin, E., Ron Shamir, A., & Mizrahi, I. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14813 · Cited by 30
“Samples from the same cows were also used for metagenomic DNA extraction as previously described (Dowd et al., 2008).”
Method
Dynamic changes of the fecal bacterial community in dairy cows during early lactation
Huang, S., Ji, S., Wang, F., Huang, J., Alugongo, G. M., & Li, S. (2020) · AMB Express · doi:10.1186/s13568-020-01106-3 · Cited by 31
Effects of the probiotic Lactobacillus animalis in murine Mycobacterium avium subspecies paratuberculosis infection
Karunasena, E., Kurkure, P. C., Lackey, R. D., McMahon, K. W., Kiernan, E. P., Graham, S. C., Alabady, M., Campos, D. L., Tatum, O. L., & Brashears, M. M. (2013) · BMC Microbiology · doi:10.1186/1471-2180-13-8 · Cited by 30
Correlation analysis of Shiga toxin-producingEscherichia colishedding and faecal bacterial composition in beef cattle
Zhao, L., Tyler, P. J., Starnes, J., Bratcher, C. L., Rankins, D. L., McCaskey, T. A., & Wang, L. (2013) · Journal of Applied Microbiology · doi:10.1111/jam.12250 · Cited by 30
“Cattle faeces contain complex bacterial communities (Dowd et al. 2008).”
Amplicon pyrosequencing reveals the soil microbial diversity associated with invasive J apanese barberry ( B erberis thunbergii DC .)
Coats, V. C., Pelletreau, K. N., & Rumpho, M. E. (2013) · Molecular Ecology · doi:10.1111/mec.12544 · Cited by 30
“Massively parallel TEFAP sequencing was performed as described previously (Dowd et al. 2008) using the Roche 454 FLX instrument with Titanium reagents, titanium procedures, a one-step PCR, mixture of Hot Start and HotStar high fidelity taq polymerases, and amplicons originating and extending from…”
Method
16S rDNA-Based Metagenomic Analysis of Bacterial Diversity Associated With Two Populations of the Kleptoplastic Sea SlugElysia chloroticaand Its Algal PreyVaucheria litorea
Devine, S. P., Pelletreau, K. N., & Rumpho, M. E. (2012) · Biological Bulletin · doi:10.1086/bblv223n1p138 · Cited by 30
“…next-generation sequencing (NGS), a greater number of bacterial symbiotic relationships are being discovered as more systems (from marine invertebrates to the human gut) are characterized (Handelsman, 2004; Kennedy et al., 2007; Dubilier et al., 2008; Ley et al., 2008; Simon and Daniel, 2011).”
Background
Effects of Dietary Linseed Oil and Propionate Precursors on Ruminal Microbial Community, Composition, and Diversity in Yanbian Yellow Cattle
Li, X. Z., Park, B. K., Shin, J. S., Choi, S. H., Smith, S. B., & Yan, C. (2015) · PLoS ONE · doi:10.1371/journal.pone.0126473 · Cited by 29
Novel Rickettsiella Bacterium in the Leafhopper Orosius albicinctus (Hemiptera: Cicadellidae)
Iasur‐Kruh, L., Weintraub, P. G., Mozes‐Daube, N., Robinson, W. E., Perlman, S. J., & Zchori‐Fein, E. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00721-13 · Cited by 29
“Pyrosequencing was performed using the Roche 454 sequencing system as previously described (26) and the primers 27F and 519R, targeting the bacterial 16S rRNA gene.”
Method
Evaluation of Automated Ribosomal Intergenic Spacer Analysis for Bacterial Fingerprinting of Rumen Microbiome Compared to Pyrosequencing Technology
Jami, E., Shterzer, N., & Mizrahi, I. (2014) · Pathogens · doi:10.3390/pathogens3010109 · Cited by 29
Different methods used to form oxygen reducing biocathodes lead to different biomass quantities, bacterial communities, and electrochemical kinetics
Rimboud, M., Barakat, M., Bergel, A., & Erable, B. (2017) · Bioelectrochemistry · doi:10.1016/j.bioelechem.2017.03.001 · Cited by 29
Insect Artifacts Are More than Just Altered Bloodstains
Rivers, D., & Geiman, T. M. (2017) · Insects · doi:10.3390/insects8020037 · Cited by 29
“Detection could be accomplished using DNA extraction followed by bacterial 16S rDNA tag encoded FLX-titanium amplicon pyrosequencing (bTEFAP), generating short DNA sequence reads [71,72].”
Method
Aerosolized bacteria and microbial activity in dental clinics during cleaning procedures
Adhikari, A., Kurella, S., Banerjee, P., & Mitra, A. (2017) · Journal of Aerosol Science · doi:10.1016/j.jaerosci.2017.09.019 · Cited by 29
Divergence of Fecal Microbiota and Their Associations With Host Phylogeny in Cervinae
Li, J., Zhan, S., Liu, X., Lin, Q., Jiang, J., & Li, X. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01823 · Cited by 29
“Apart from deer, Ruminococcus was observed in many other species, e.g., alpaca, cattle, goat, horse, sheep, pika, and rhinoceros (Dowd et al., 2008; Kim et al., 2011; Robert, 2012; Li et al., 2017; Neumann et al., 2017; O’Donnell et al., 2017; Kohl et al., 2018b).”
Background
Environmental DNA reveals landscape mosaic of wetland plant communities
Shackleton, M. E., Rees, G. N., Watson, G., Campbell, C. J., & Nielsen, D. L. (2019) · Global Ecology and Conservation · doi:10.1016/j.gecco.2019.e00689 · Cited by 29
OGG1 deficiency alters the intestinal microbiome and increases intestinal inflammation in a mouse model
Simon, H. M., Vartanian, V. L., Wong, M. H., Nakabeppu, Y., Sharma, P., Lloyd, R. S., & Sampath, H. (2020) · PLoS ONE · doi:10.1371/journal.pone.0227501 · Cited by 29
“In collaboration with the Mouse Metabolic Phenotyping Center (MMPC) at UC Davis, the V1-V3 variable region of the 16S rRNA gene was examined by bacterial tag encoded FLX-Titanium amplicon pyrosequencing (bTEFAP) as described [61].”
Method
The Effect of Transitioning between Feeding Methods on the Gut Microbiota Dynamics of Yaks on the Qinghai–Tibet Plateau
Zhang, X., Xu, T., Wang, X., Geng, Y., Liu, H., Hu, L., Zhao, N., Kang, S., Zhang, W.-M., & Xu, S. (2020) · Animals · doi:10.3390/ani10091641 · Cited by 29
Diversity of freshwaterEpsilonproteobacteriaand dark inorganic carbon fixation in the sulphidic redoxcline of a meromictic karstic lake
Noguerola, I., Picazo, A., Llirós, M., Camacho, A., & Borrego, C. (2015) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiv086 · Cited by 29
“Pyrosequencing of total extracted genomic DNA from selected depths and seasonswas performed at Research and Testing Laboratory facilities (RTL) (TX, USA) using Roche 454 FLX-Titanium technology (Dowd et al. 2008).”
Method
The role of the bacterial community in the nutritional ecology of the bulb mite Rhizoglyphus robini (Acari: Astigmata: Acaridae)
Zindel, R., Ofek, M., Minz, D., PALEVSKY, E., Zchori‐Fein, E., & Aebi, A. (2013) · The FASEB Journal · doi:10.1096/fj.12-216242 · Cited by 29
Bacterial associates of seed-parasitic wasps (Hymenoptera: Megastigmus)
Paulson, A. R., von Aderkas, P., & Perlman, S. J. (2014) · BMC Microbiology · doi:10.1186/s12866-014-0224-4 · Cited by 29
“The methods used for bTEFAP are previously described in Palavesam et al. (2012) and Shange et al. (2012) [116,117] and were originally described by Dowd et al. (2008) [118].”
Method
Bacterial diversity of the rock-water interface in an East Antarctic freshwater ecosystem, Lake Tawani(P)†
Huang, J. P., Swain, A. K., THACKER, R. W., Ravindra, R., Andersen, D. T., & Bej, A. K. (2013) · Aquatic Biosystems · doi:10.1186/2046-9063-9-4 · Cited by 29
“Oligonucleotide primers 341F (5’–CCT ACG GGA GGC AGC AG–3’ [33] and 907R (5’–CCG TCA ATT CMT TTG AGT TT–3’ [34] that targets the V3-V5 region of the 16S rRNA [35] were used for pyrosequencing.”
Method
A formation water-based nutrient recipe for potentially increasing methane release from coal in situ
Bi, Z., Ji, Z., Park, S., Harpalani, S., & Liang, Y. (2017) · Fuel · doi:10.1016/j.fuel.2017.08.008 · Cited by 29
Metagenomic analysis of the fecal microbiomes from Escherichia coli O157:H7-shedding and non-shedding cows on a single dairy farm
Salaheen, S., Kim, S. W., Karns, J. S., Hovingh, E., Haley, B. J., & Kessel, J. A. S. V. (2019) · Food Control · doi:10.1016/j.foodcont.2019.03.022 · Cited by 31
Microbial Stimulation and Succession following a Test Well Injection Simulating CO₂ Leakage into a Shallow Newark Basin Aquifer
O'Mullan, G. D., Dueker, M. E., Clauson, K., Yang, Q., Kelsey, U., Zakharova, N. V., Matter, J., Stute, M., Takahashi, T., & Goldberg, D. S. (2015) · PLoS ONE · doi:10.1371/journal.pone.0117812 · Cited by 28
N2 Gas Flushing Alleviates the Loss of Bacterial Diversity and Inhibits Psychrotrophic Pseudomonas during the Cold Storage of Bovine Raw Milk
Gschwendtner, S., Alatossava, T., Kublik, S., Fuka, M. M., Schloter, M., & Munsch-Alatossava, P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0146015 · Cited by 28
“Alistipes bacteria were detected in cattle feces [33] and bacteria belonging to Chryseobacterium were previously isolated from bovine milk [34–36].”
Background
Biotransformation of food spice curcumin by gut bacteriumBacillus megateriumDCMB-002 and its pharmacological implications
An, C.-Y., Sun, Z., Shen, L., & Ji, H. (2017) · Food & Nutrition Research · doi:10.1080/16546628.2017.1412814 · Cited by 28
“formed using a molecular biological protocol by DNA amplification and sequencing of the 16S rDNA as described previously [18].”
Method
Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities
Gaete, A., Pulgar, R., Hödar, C., Maldonado, J. E., Pavéz, L., Zamorano, D., Pastenes, C., González, M., Franck, N., & Mandaković, D. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.688533 · Cited by 29
“Processing of Illumina Sequence Data Raw amplicon sequences were processed and analyzed following previously described protocols (Dowd et al., 2008; Handl et al., 2011).”
Method
Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing
Mtshali, K., Khumalo, Z. T. H., Kwenda, S., Ismail, A., & Thekisoe, O. M. M. (2022) · PLoS ONE · doi:10.1371/journal.pone.0273799 · Cited by 28
Alteration of digestive tract microbiome in neonatal Holstein bull calves by bacitracin methylene disalicylate treatment and scours1
Xie, G., Duff, G. C., Hall, L. W., Allen, J. D., Burrows, C. D., Bernal-Rigoli, J. C., Dowd, S. E., Guerriero, V., & Yeoman, C. J. (2013) · Journal of Animal Science · doi:10.2527/jas.2013-6304 · Cited by 28
Changes in soil microbial communities as affected by intensive cattle husbandry
Elhottová, D., Koubová, A., Šimek, P., Cajthaml, T., Jirout, J., Esperschuetz, J., Schloter, M., & Gattinger, A. (2012) · Applied Soil Ecology · doi:10.1016/j.apsoil.2012.03.009 · Cited by 28
Disruption of Pten Speeds Onset and Increases Severity of Spontaneous Colitis in Il10−/− Mice
Im, E., Jung, J., Pothoulakis, C., & Rhee, S. H. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.05.034 · Cited by 28
Contrasting histories of microcystin-producing cyanobacteria in two temperate lakes as inferred from quantitative sediment DNA analyses
Pilon, S., Zastepa, A., Taranu, Z. E., Gregory‐Eaves, I., Racine, M., Blais, J. M., Poulain, A. J., & Pick, F. R. (2019) · Lake and Reservoir Management · doi:10.1080/10402381.2018.1549625 · Cited by 28
Driving forces shaping the microbial ecology in meat packing plants
Yang, X., Narváez-Bravo, C. A., & Zhang, P. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1333696 · Cited by 33
Bacterial diversity differences along an epigenic cave stream reveal evidence of community dynamics, succession, and stability
Brannen-Donnelly, K. M., & Engel, A. S. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00729 · Cited by 27
“…6 | Article 729 location and month were homogenized prior to purification, barcoding, and amplicon pyrosequencing using a Roche 454 FLX Titanium instrument and reagents, as described in Dowd et al. (2008), at the Molecular Research LP (MrDNA) laboratory (www.mrdnalab.com; Shallowater, Texas, USA).”
Method
Role of Organic Carbon Sources and Sulfate in Controlling Net Methylmercury Production in Riverbank Sediments of the South River, VA (USA)
Paulson, K. M. A., Ptacek, C. J., Blowes, D. W., Gould, W. D., Ma, J., Landis, R. C., & Dyer, J. A. (2016) · Geomicrobiology Journal · doi:10.1080/01490451.2016.1247483 · Cited by 27
“Operational taxonomic units (OTUs) were defined as sequences clustering at 3% divergence, and the chimeras and singleton sequences were removed (Dowd et al. 2008a, b; Edgar 2010).”
Background
Distinct systemic microbiome and microbial translocation are associated with plasma level of anti-CD4 autoantibody in HIV infection
Xu, W., Luo, Z., Alekseyenko, A. V., Martin, L., Wan, Z., Ling, B., Qin, Z., Heath, S. L., Maas, K. R., Cong, X. S., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-31116-y · Cited by 27
Associations between bacterial communities and microplastics from surface seawater of the Northern Patagonian area of Chile
Aguila‐Torres, P., González, M., Maldonado, J. E., Miranda, R. M., Zhang, L., González‐Stegmaier, R., Rojas, L. A., & Gaete, A. (2022) · Environmental Pollution · doi:10.1016/j.envpol.2022.119313 · Cited by 26
Improvement of RNA-SIP by pyrosequencing to identify putative 4-n-nonylphenol degraders in activated sludge
Zemb, O., Lee, M., Gutierrez-Zamora, M.-L., Hamelin, J., Coupland, K., Hazrin-Chong, N. H., Taleb, I., & Manefield, M. J. (2011) · Water Research · doi:10.1016/j.watres.2011.10.047 · Cited by 27
DNA extraction from bovine faeces: current status and future trends
Rapp, D. (2009) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2009.04606.x · Cited by 27
“These components include diverse micro-organisms and a high (47–68%) fibre content because of undigested residues of herbivorous matter (cellulose, hemicelluloses and lignin), which has passed through the animal’s gut (Holloway et al. 1981; Haynes and Williams 1993; Dowd et al. 2008).”
Background
Development and validation of a high-resolution mass-spectrometry-based method to study the long-term stability of natural and synthetic glucocorticoids in faeces.
Clercq, N. D., Bussche, J. V., Croubels, S., Delahaut, P., & Vanhaecke, L. (2014) · Journal of Chromatography A · doi:10.1016/j.chroma.2014.02.033 · Cited by 27
Acidobacteriaappear to dominate the microbiome of two sympatric Caribbean Sponges and one Zoanthid
O’Connor-Sánchez, A., Rivera-Domínguez, A. J., Santos-Briones, C. D. L., López-Aguiar, L. K., Peña-Ramírez, Y. J., & Prieto‐Davó, A. (2014) · Biological Research · doi:10.1186/0717-6287-47-67 · Cited by 27
“Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) was performed as described previously using bacterial universal primers Gray28F (5 ’ - TTTGATCNTGGCTCAG-3 ’ ) and Gray519R (5 ’ -GTNTT ACNGCGGCKGCTG-3 ’ ) primers [22].”
Bringing microbial diversity into focus: high‐resolution analysis of iron mats from the Lō‘ihi Seamount
Scott, J. J., Glazer, B. T., & Emerson, D. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13607 · Cited by 25
Response of Beef Cattle Fecal Microbiota to Grazing on Toxic Tall Fescue
Mote, R. S., Hill, N. S., Skarlupka, J. H., Turner, Z. B., Sanders, Z. P., Jones, D. P., Suen, G., & Filipov, N. M. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.00032-19 · Cited by 27
“Notably, in beef cattle, the influence of feed additives and/or diet on the rumen and fecal microbial communities has been evaluated (10–13), and ubiquitous and foodborne pathogenic bacteria were identified in their fecal matter (14).”
Background
Effect of volatile fatty acids mixtures on the simultaneous photofermentative production of hydrogen and polyhydroxybutyrate
Cardeña, R., Vazquez, I. V., & Buitrón, G. (2016) · Bioprocess and Biosystems Engineering · doi:10.1007/s00449-016-1691-9 · Cited by 27
Surveys for maternally-inherited endosymbionts reveal novel and variable infections within solitary bee species
Saeed, A., & White, J. A. (2015) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2015.09.011 · Cited by 26
Tri-Party Underground Symbiosis between a Weevil, Bacteria and a Desert Plant
Shelef, O., Helman, Y., Friedman, A., Behar, A., & Rachmilevitch, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076588 · Cited by 26
Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing
Festa, S., Macchi, M., Cortés, F., Morelli, I. S., & Coppotelli, B. M. (2016) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw125 · Cited by 26
“The outputs were compiled and validated using taxonomic distance methods (Dowd et al. 2008).”
Method
Metagenomic and PCR-Based Diversity Surveys of [FeFe]-Hydrogenases Combined with Isolation of Alkaliphilic Hydrogen-Producing Bacteria from the Serpentinite-Hosted Prony Hydrothermal Field, New Caledonia
Mei, N., Postec, A., Monnin, C., Pelletier, B., Payri, C. E., Ménèz, B., Frouin, E., Ollivier, B., Erauso, G., & Quéméneur, M. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01301 · Cited by 25
“The mixtures of 16S rRNA gene amplicons were generated from a 341F/815R bacterial primer set, as previously described by Dowd et al. (2008), and were sequenced on a 454 GSFLX Titanium sequencer (Roche Life Sciences, USA) by the Molecular Research Laboratory (Texas, USA).”
Method
Characterisation of above-ground endophytic and soil fungal communities associated with dieback-affected and healthy plants in five exotic invasive species
Raghavendra, A., Bissett, A. B., Thrall, P. H., Morin, L., Steinrucken, T. V., Galea, V. J., Goulter, K. C., & van Klinken, R. D. (2017) · Fungal ecology · doi:10.1016/j.funeco.2017.01.003 · Cited by 26
Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis
Hussein, E. I., Jacob, J. H., Shakhatreh, M. A. K., Al‐razaq, M. A. A., Juhmani, A.-S. F. A., & Cornelison, C. T. (2017) · MicrobiologyOpen · doi:10.1002/mbo3.521 · Cited by 26
Metabarcoding analysis of the fungal biodiversity associated with Castaño Overa Glacier – Mount Tronador, Patagonia, Argentina
Saito, R. A. D., Connell, L. B., Rodriguez, R. J., Redman, R. S., Libkind, D., & de García, V. (2018) · Fungal ecology · doi:10.1016/j.funeco.2018.07.006 · Cited by 26
Conventional and omics approaches shed light on Halitzia cheese, a long-forgotten white-brined cheese from Cyprus
Papademas, P., Aspri, M., Μάριου, Μ., Dowd, S. E., Κάζου, Μ., & Tsakalidou, E. (2019) · International Dairy Journal · doi:10.1016/j.idairyj.2019.06.010 · Cited by 26
Enhancing fermentative hydrogen production from sucrose
Perera, K. R. J., & Nirmalakhandan, N. N. (2010) · Bioresource Technology · doi:10.1016/j.biortech.2010.06.145 · Cited by 26
Effect of ensiled mulberry leaves and sun-dried mulberry fruit pomace on the fecal bacterial community composition in finishing steers
Li, Y., Meng, Q., Zhou, B., & Zhou, Z. (2017) · BMC Microbiology · doi:10.1186/s12866-017-1011-9 · Cited by 25
Changes in motor behavior, neuropathology, and gut microbiota of a Batten disease mouse model following administration of acidified drinking water
Johnson, T. B., Langin, L. M., Zhao, J., Weimer, J. M., Pearce, D. A., & Kovács, A. (2019) · Scientific Reports · doi:10.1038/s41598-019-51488-z · Cited by 25
Evaluation of fecal fermentation profile and bacterial community in organically fed dairy cows consuming forage-rich diets with different particle sizes
Castillo‐Lopez, E., Haselmann, A., Petri, R. M., Knaus, W., & Zebeli, Q. (2020) · Journal of Dairy Science · doi:10.3168/jds.2019-18036 · Cited by 25
Increasing aridity shapes beta diversity and the network dynamics of the belowground fungal microbiome associated with Opuntia ficus-indica
Gargouri, M., Karray, F., Chebaane, A., Mhiri, N., Partida‐Martínez, L. P., Sayadi, S., & Mliki, A. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.145008 · Cited by 25
Addition of Activated Carbon into a Cattle Diet to Mitigate GHG Emissions and Improve Production
Al-Azzawi, M., Bowtell, L., Hancock, K. R., & Preston, S. (2021) · Sustainability · doi:10.3390/su13158254 · Cited by 30
Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert
Mandaković, D., Aguado‐Norese, C., García-Jiménez, B., Christian Hodar, Q., Maldonado, J. E., Gaete, A., Latorre, M., Wilkinson, M. D., Gutiérrez, R. A., Cavieres, L. A., et al. (2023) · Environmental Microbiome · doi:10.1186/s40793-023-00486-w · Cited by 25
Evaluation of culture-based techniques and 454 pyrosequencing for the analysis of fungal diversity in potting media and organic fertilizers
Al-Sadi, A. M., Al-Mazroui, S. S., & Phillips, A. J. L. (2015) · Journal of Applied Microbiology · doi:10.1111/jam.12854 · Cited by 25
“Taxonomic distance methods (Dowd et al. 2008a,b) were used to validate the outputs based on a 97% cut off.”
Method
Internal Extracellular Bacteria of Diaphorina citri Kuwayama (Hemiptera: Psyllidae), the Asian Citrus Psyllid
Kolora, L. D., Powell, C. M., Hunter, W. B., Bextine, B. R., & Lauzon, C. R. (2015) · Current Microbiology · doi:10.1007/s00284-015-0774-1 · Cited by 25
Molecular and culture dependent characterization of endolithic bacteria in two beach sand samples and description of Rhizobium endolithicum sp. nov.
Parag, B., Sasikala, C., & Ramana, C. V. (2013) · Antonie van Leeuwenhoek · doi:10.1007/s10482-013-0046-7 · Cited by 25
“The small fragments were removed by using Agencourt Ampure Beads (Beckman Coulter, CA, USA) Bacterial tagencoded FLX-Titanium amplicon pyrosequencing (bTEFAP) was performed (as described by Dowd et al. 2008). In preparation for FLX-Titanium sequencing (Roche, Nutley, New Jersey), DNA fragment sizes 1236 Antonie van Le…”
Method
Bacterial Community Analysis of Beef Cattle Feedlots Reveals That Pen Surface Is Distinct from Feces
Durso, L. M., Harhay, G. P., Smith, T. P. L., Bono, J. L., DeSantis, T. Z., & Clawson, M. L. (2011) · Foodborne Pathogens and Disease · doi:10.1089/fpd.2010.0774 · Cited by 25
“These numbers are signiﬁcantly higher than reports from cattle feces which identiﬁed 142, or 478 bacterial species (Dowd et al. , 2008; Durso et al. , 2010) but below the estimated 2000 found in Minnesota soil (Schloss and Handelsman, 2006).”
Effect of Feeding Bacillus subtilis natto on Hindgut Fermentation and Microbiota of Holstein Dairy Cows
Song, D., Kang, H.-S., Wang, J., Peng, H., & Bu, D. (2014) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.2013.13522 · Cited by 25
A simple medium modification for isolation, growth and enumeration of Acidithiobacillus thiooxidans (syn. Thiobacillus thiooxidans) from water samples
Starosvetsky, J., Zukerman, U., & Armon, R. H. (2012) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2012.11.009 · Cited by 25
“After resolving based upon these parameters, the percentage of each bacterial and fungal ID was individually analyzed for each sample providing relative abundance information within and among the individual samples based upon relative numbers of reads within each sample (Dowd et al., 2008).”
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

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

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks