Ruminal metagenomic analyses of goat data reveals potential functional microbiota by supplementation with essential oil-cobalt complexes
Open accessAbstract
BACKGROUND: Essential Oils (EO) are complex mixtures of plant secondary metabolites that have been proposed as promising feed additives for mitigating methane and ammonia emissions. We have previously demonstrated that Essential Oil-Cobalt (EOC) supplementation resulted in increased average daily gain and improved phenotypes (cashmere fiber traits, carcass weight, and meat quality) when cashmere goats received supplementation at approximately 2 mg/kg of body weight. However, the ruminal microbiological effects of EO remain poorly understood with regard to the extent to which ruminal populations can adapt to EO presence as feed ingredients. The effects of varying levels of EO require additional study. RESULTS: In this study, we conducted metagenomic analyses using ruminal fluid samples from three groups (addition of 0, 52, and 91 mg) to evaluate the influence of dietary EOC supplementation on goat rumen bacterial community dynamics. EOC addition resulted in changes of ruminal fermentation types and the EOC dose strongly impacted the stability of ruminal microbiota. The Bacteroides sp. and Succinivibrio sp. type bacterial community was positively associated with improved volatile fatty acid production when the diet was supplemented with EOC. CONCLUSIONS: A clear pattern was found that reflected rapid fermentative improvement in the rumen, subsequent to butyrate metabolism and EOC based feed additives may affect rumen microbes to further improve feed conversion. This observation indicates that EOC can be safely used to enhance animal productivity and to reduce ammonia and waste gas emissions, thus positively impacting the environment.
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
Cites
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?
Functional prediction pathway analysis exhibited upregulation of lipid and carbohydrate pathways by essential oils.
“Moreover, functional prediction pathway analysis exhibited upregulation of lipid and carbohydrate pathways by EO (233).”
From Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet–Microbe Interaction (2020) · cites this paper as [233]
The Results section (‘Functional characterization of the EOC diet group microbiome’; page unavailable) reports significant enrichment of carbohydrate- and lipid-metabolism gene categories in goats given essential oil–cobalt complexes. This supports a change in those predicted functions, but the passage does not establish that both pathways were upregulated, and the treatment was not essential oils alone. (LLM, conf=0.84)
Experimental — accuracy not yet measuredEssential oil-cobalt complexes have shown positive effects in ruminants by enhancing productive performance while decreasing NH3 emissions.
“Essential oil–cobalt complexes have shown positive effects in ruminants by enhancing productive performance while decreasing NH3 emissions (233).”
From Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet–Microbe Interaction (2020) · cites this paper as [233]
The Results (Microbial metabolites and morphology in the goat rumen; page unavailable) report significantly increased average daily gain and reduced ruminal NH3-N production with EOC supplementation. The Conclusions suggest EOC could reduce ammonia emissions, but the reported measurement is ruminal ammonia production, not emissions. The claim overstates that part as an observed effect. (LLM, conf=0.85)
Experimental — accuracy not yet measuredBacteroides sp. and Succinivibrio sp. showed a positive correlation with enhanced volatile fatty acid production in essential oil-supplemented groups.
“It was revealed that Bacteroides sp. and Succinivibrio sp. showed a positive correlation with enhanced VFA production in supplemented groups.”
From Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet–Microbe Interaction (2020) · cites this paper as [233]
Metagenomic analysis of goat rumen revealed that essential oil cobalt complexes significantly manipulated the structural and functional profile of rumen microbiota.
“Recently, metagenomic analysis of goat rumen revealed that EO cobalt complexes significantly manipulated the structural and functional profile of rumen microbiota.”
From Phytogenic Additives Can Modulate Rumen Microbiome to Mediate Fermentation Kinetics and Methanogenesis Through Exploiting Diet–Microbe Interaction (2020) · cites this paper as [233]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Fast and sensitive protein alignment using DIAMOND
Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201 · see citing works
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works
Self-citationCd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,994 · see citing works
Changes of Intestinal Functions in Liver Cirrhosis
Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,820 · see citing works
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. (2012) · GigaScience · doi:10.1186/2047-217x-1-18 · Cited by 5,274 · see citing works
Self-citationProteobacteria: Microbial signature of dysbiosis in gut microbiota
Shin, N.-R., Whon, T. W., & Bae, J.-W. (2015) · Trends in Biotechnology · doi:10.1016/j.tibtech.2015.06.011 · Cited by 3,954 · see citing works
Modified Reagents for Determination of Urea and Ammonia
Chaney, A. L., & Marbach, E. P. (1962) · Clinical Chemistry · doi:10.1093/clinchem/8.2.130 · Cited by 3,941 · see citing works
Alterations of the human gut microbiome in liver cirrhosis
Qin, N., Yang, F., Li, A., Prifti, E., Chen, Y., Shao, L., Guo, J., Le Chatelier, E., Yao, J., Wu, L., et al. (2014) · Nature · doi:10.1038/nature13568 · Cited by 2,177 · see citing works
Hobson, P. N., & Stewart, C. S. (1997) · Springer eBooks · doi:10.1007/978-94-009-1453-7 · Cited by 2,146 · see citing works
Huson, D. H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra, S., Ruscheweyh, H.-J., & Tappu, R. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004957 · Cited by 1,761 · see citing works
Integrative analysis of environmental sequences using MEGAN4Preprint
Huson, D. H., Mitra, S., Ruscheweyh, H., Weber, N., & Schuster, S. C. (2011) · Genome Research · doi:10.1101/gr.120618.111 · Cited by 1,534 · see citing works
Gut microbiome development along the colorectal adenoma-carcinoma sequence
Feng, Q., Liang, S., Jia, H., Stadlmayr, A., Tang, L., Lan, Z., Zhang, D., Xia, H., Xu, X., Jie, Z., et al. (2015) · Nature Communications · doi:10.1038/ncomms7528 · Cited by 1,506 · see citing works
Self-citationGSEA-P : a desktop application for Gene Set Enrichment Analysis
Subramanian, A., Kuehn, H., Gould, J., Tamayo, P., & Mesirov, J. P. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm369 · Cited by 1,380 · see citing works
Stability of Essential Oils: A Review
Turek, C., & Stintzing, F. C. (2013) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12006 · Cited by 1,315 · see citing works
Bickhart, D. M., Rosen, B. D., Koren, S., Sayre, B. L., Hastie, A. R., Chan, S., Lee, J., Lam, E. T., Liachko, I., Sullivan, S. T., et al. (2017) · Nature Genetics · doi:10.1038/ng.3802 · Cited by 620 · see citing works
Effect of Probiotics/Prebiotics on Cattle Health and Productivity
Uyeno, Y., Shigemori, S., & Shimosato, T. (2015) · Microbes and Environments · doi:10.1264/jsme2.me14176 · Cited by 462 · see citing works
Colonization-induced host-gut microbial metabolic interaction
Claus, S. P., Ellero, S. L., Berger, B., Krause, L., Bruttin, A., Molina, J., Paris, A., Want, E. J., de Waziers, I., Cloarec, O., et al. (2011) · mBio · doi:10.1128/mbio.00271-10 · Cited by 414 · see citing works
Effects of essential oils on ruminal microorganisms and their protein metabolism
McIntosh, F. M., Williams, P., Losa, R., Wallace, R. J., Beever, D. A., & Newbold, C. J. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.8.5011-5014.2003 · Cited by 412 · see citing works
Essential oils and opportunities to mitigate enteric methane emissions from ruminants
Benchaar, C., & Greathead, H. M. R. (2011) · Animal Feed Science and Technology · doi:10.1016/j.anifeedsci.2011.04.024 · Cited by 357 · see citing works
Barns, S. M., Cain, E. C., Sommerville, L., & Kuske, C. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02012-06 · Cited by 343 · see citing works
Critical evaluation of essential oils as rumen modifiers in ruminant nutrition: a review
Cobellis, G., Trabalza-Marinucci, M., & Yu, Z. (2016) · Science of The Total Environment · doi:10.1016/j.scitotenv.2015.12.103 · Cited by 291 · see citing works
Rumen microbial (meta)genomics and its application to ruminant production
Morgavi, D. P., Kelly, W. J., Janssen, P. H., & Attwood, G. T. (2012) · animal · doi:10.1017/s1751731112000419 · Cited by 278 · see citing works
VII.—The Anatomy of Follicles Producing Wool-Fibres, with special reference to Keratinization
AUBER, L. (1952) · Transactions of the Royal Society of Edinburgh · doi:10.1017/s0080456800009285 · Cited by 251 · see citing works
The role of essential trace elements in embryonic and fetal development in livestock
Hostetler, C. E., Kincaid, R. L., & Mirando, M. A. (2003) · The Veterinary Journal · doi:10.1016/s1090-0233(02)00310-6 · Cited by 246 · see citing works
LaPara, T. M., Nakatsu, C. H., Pantea, L. M., et al. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.9.3951-3959.2000 · Cited by 233 · see citing works
Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies
Pope, P. B., Smith, W. J. M., Denman, S. E., Tringe, S. G., Barry, K., Hugenholtz, P., McSweeney, C. S., McHardy, A. C., & Morrison, M. (2011) · Science · doi:10.1126/science.1205760 · Cited by 225 · see citing works
Auffret, M. D., Dewhurst, R. J., Duthie, C.-A., Rooke, J. A., Wallace, R. J., Freeman, T. C., Stewart, R., Watson, M., & Roehe, R. (2017) · Microbiome · doi:10.1186/s40168-017-0378-z · Cited by 215 · see citing works
Members of the phylumAcidobacteriaare dominant and metabolically active in rhizosphere soil
Lee, S.-H., Ka, J.-O., & Cho, J.-C. (2008) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2008.01232.x · Cited by 199 · see citing works
Effect of dietary oregano oil supplementation on lamb meat characteristics
Simitzis, P., Deligeorgis, S. G., Bizelis, J. A., Dardamani, A., Theodosiou, I., & Fegeros, K. (2007) · Meat Science · doi:10.1016/j.meatsci.2007.09.005 · Cited by 197 · see citing works
Effects of essential oils and their components on in vitro rumen microbial fermentation
Benchaar, C., Chaves, A. V., Fraser, G. R., Beauchemin, K. A., & McAllister, T. A. (2007) · Canadian Journal of Animal Science · doi:10.4141/cjas07012 · Cited by 161 · see citing works
Панкратов, Т. А., & Dedysh, S. N. (2010) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.021824-0 · Cited by 146 · see citing works
Variation in soil net mineralization rates with dissolved organic carbon additions
Magill, A., & Aber, J. (2000) · Soil Biology and Biochemistry · doi:10.1016/s0038-0717(99)00186-8 · Cited by 135 · see citing works
Pepper, M. R., & Black, M. M. (2011) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2011.05.005 · Cited by 123 · see citing works
Evidence of Increased Diversity of Methanogenic Archaea with Plant Extract Supplementation
Ohene-Adjei, S., Chaves, A. V., McAllister, T. A., Benchaar, C., Teather, R. M., & Forster, R. J. (2007) · Microbial Ecology · doi:10.1007/s00248-007-9340-0 · Cited by 119 · see citing works
Hair follicle group and skin follicle population of Australian Merino sheep
Carter, H., & Clarke, W. (1957) · Australian Journal of Agricultural Research · doi:10.1071/ar9570091 · Cited by 113 · see citing works
Hobel, C. F. V., Marteinsson, V., Hreggviðsson, G. Ó., et al. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.5.2771-2776.2005 · Cited by 99 · see citing works
Patra, A. K., & Yu, Z. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00297 · Cited by 92 · see citing works
Hoskin, S. O., Stafford, K. J., & Barry, T. N. (1995) · The Journal of Agricultural Science · doi:10.1017/s0021859600072956 · Cited by 37 · see citing works
Lei, Z., Zhang, K., Li, C., Wu, J., Davis, D. I., Casper, D. P., Jiang, H., Jiao, T., Wang, X., & Wang, J. (2018) · Scientific Reports · doi:10.1038/s41598-018-29897-3 · Cited by 33 · see citing works
Self-citationMobile genetic elements in the bacterial phylum Acidobacteria
Challacombe, J. F., & Kuske, C. R. (2012) · Mobile Genetic Elements · doi:10.4161/mge.21943 · Cited by 26 · see citing works
Essential oils effect on rumen fermentation and biohydrogenation under in vitro conditions
Günal, M., Ishlak, A., AbuGhazaleh, A. A., & Khattab, W. (2014) · Czech Journal of Animal Science · doi:10.17221/7708-cjas · Cited by 24 · see citing works
Agrawal, A. R., Karim, S., Kumar, R., SAHOO, A., & John, P. A. (2014) · Cited by 24 · see citing works
Dietary Possibilities to Mitigate Rumen Methane and Ammonia Production
Szumacher‐Strabel, M., & Cielak, A. (2012) · InTech eBooks · doi:10.5772/32105 · Cited by 17 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Hassan, F.-U., Arshad, M. A., Ebeid, H. M., Rehman, M. S.-U., Khan, M. S., Shahid, S., & Yang, C. (2020) · Frontiers in Veterinary Science · doi:10.3389/fvets.2020.575801 · Cited by 160 · see citing works
- Authors
- Lei, Z., Zhang, K., Li, C., Jiao, T., Wu, J., Wei, Y., Tian, K., Li, C., Tang, D., Davis, D. I., Casper, D. P., Jiang, H., Wang, X., & Wang, J.
- Affiliations
- Gansu Agricultural University (CN)
- Northwest A&F University (CN)
- Gansu Academy of Agricultural Sciences (CN)
- Xinjiang Academy of Animal Science (CN)
- Novo Nordisk Canada (Canada) (CA)
- Laboratoire des applications Thérapeutiques des Ultrasons (FR)
- Corresponding author
- Wang, Jianfu
- ORCID
- Venue
- BMC Microbiology
- Published
- 2019-02-04
- Volume
- 19
- Issue
- 1
- Pages
- 30-30
- ISSN
- 1471-2180 (ISSN-L)
- PMC
- PMC6362596
- OpenAlex
- W2915235119
- Cited by
- 48
- References
- 43
- Citations by year
- 2026: 3 · 2025: 8 · 2024: 5 · 2023: 9 · 2022: 8 · 2021: 10 · 2020: 3 · 2019: 2
- FWCI
- 8.06
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Microbiology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Agro-scientific Research in the Public Interest (No. 201503134, 201303059)
- China Agriculture Research System (No. CARS-39-18)
- the major science and technology projects of Gansu Province (No. 17ZD2NC020)
- Lanzhou Science & Technology Bureau (No. 2012-2-159)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Ruminant Nutrition and Digestive Physiology
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Nutrition and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- rumen microbiota, cashmere goats, feed additives, rumen fermentation, volatile fatty acids, Bacteroides, Succinivibrio, butyrate metabolism, methane mitigation, ammonia emissions, microbial community stability, dose-dependent effects
- MeSH terms
- Animals, Animal Feed, Cobalt, Digestion, Fatty Acids, Volatile, Fermentation, Goats, Male, Methane, Oils, Volatile, Rumen, Dietary Supplements, Metagenomics, Microbiota
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
