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For: Stewart RD, Auffret MD, Warr A, Wiser AH, Press MO, Langford KW, Liachko I, Snelling TJ, Dewhurst RJ, Walker AW, Roehe R, Watson M. Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. Nat Commun 2018;9:870. [PMID: 29491419 PMCID: PMC5830445 DOI: 10.1038/s41467-018-03317-6] [Citation(s) in RCA: 332] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/05/2018] [Indexed: 12/15/2022]  Open
Number Cited by Other Article(s)
151
Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart. PLoS Comput Biol 2022;18:e1009947. [PMID: 35259160 PMCID: PMC8932566 DOI: 10.1371/journal.pcbi.1009947] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/18/2022] [Accepted: 02/21/2022] [Indexed: 02/07/2023]  Open
152
Stamboulian M, Canderan J, Ye Y. Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species. PLoS Comput Biol 2022;18:e1009397. [PMID: 35302987 PMCID: PMC8967034 DOI: 10.1371/journal.pcbi.1009397] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/30/2022] [Accepted: 02/15/2022] [Indexed: 12/26/2022]  Open
153
The microbiome of the buffalo digestive tract. Nat Commun 2022;13:823. [PMID: 35145088 PMCID: PMC8831627 DOI: 10.1038/s41467-022-28402-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 01/11/2022] [Indexed: 12/11/2022]  Open
154
Ivanova V, Chernevskaya E, Vasiluev P, Ivanov A, Tolstoganov I, Shafranskaya D, Ulyantsev V, Korobeynikov A, Razin SV, Beloborodova N, Ulianov SV, Tyakht A. Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients. Front Microbiol 2022;12:770323. [PMID: 35185811 PMCID: PMC8851603 DOI: 10.3389/fmicb.2021.770323] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/25/2021] [Indexed: 01/02/2023]  Open
155
Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice. Microorganisms 2022;10:microorganisms10020328. [PMID: 35208784 PMCID: PMC8879337 DOI: 10.3390/microorganisms10020328] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023]  Open
156
Xue MY, Wu JJ, Xie YY, Zhu SL, Zhong YF, Liu JX, Sun HZ. Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing. MICROBIOME 2022;10:11. [PMID: 35057854 PMCID: PMC8772221 DOI: 10.1186/s40168-021-01211-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/07/2021] [Indexed: 05/23/2023]
157
Chen H, Chu JSC, Chen J, Luo Q, Wang H, Lu R, Zhu Z, Yuan G, Yi X, Mao Y, Lu C, Wang Z, Gu D, Jin Z, Zhang C, Weng Z, Li S, Yan X, Yang R. Insights into the Ancient Adaptation to Intertidal Environments by Red Algae Based on a Genomic and Multiomics Investigation of Neoporphyra haitanensis. Mol Biol Evol 2022;39:msab315. [PMID: 34730826 PMCID: PMC8752119 DOI: 10.1093/molbev/msab315] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
158
Pereira AM, de Lurdes Nunes Enes Dapkevicius M, Borba AES. Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission? Anim Microbiome 2022;4:5. [PMID: 34991722 PMCID: PMC8734291 DOI: 10.1186/s42523-021-00153-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022]  Open
159
Metagenomes Binning Using Proximity-Ligation Data. Methods Mol Biol 2022;2301:163-181. [PMID: 34415535 DOI: 10.1007/978-1-0716-1390-0_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
160
Zeng Y, Pu Y, Niu L, Deng J, Zeng D, Amato K, Li Y, Zhou Y, Lin Y, Wang J, Wu L, Chen B, Pan K, Jing B, Ni X. Comparison of gastrointestinal microbiota in golden snub-nosed monkey (Rhinopithecus roxellanae), green monkey (Chlorocebus aethiops sabaeus), and ring-tailed lemur (Lemur catta) by high throughput sequencing. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]  Open
161
Chibani CM, Mahnert A, Borrel G, Almeida A, Werner A, Brugère JF, Gribaldo S, Finn RD, Schmitz RA, Moissl-Eichinger C. A catalogue of 1,167 genomes from the human gut archaeome. Nat Microbiol 2022;7:48-61. [PMID: 34969981 PMCID: PMC8727293 DOI: 10.1038/s41564-021-01020-9] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022]
162
Perlman D, Martínez-Álvaro M, Moraïs S, Altshuler I, Hagen LH, Jami E, Roehe R, Pope PB, Mizrahi I. Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development. Annu Rev Anim Biosci 2021;10:177-201. [PMID: 34941382 DOI: 10.1146/annurev-animal-013020-020412] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
163
Sapountzis P, Teseo S, Otani S, Aarestrup FM, Forano E, Suen G, Tsiamis G, Haley B, Van Kessel JA, Huws SA. FI: The Fecobiome Initiative. Foodborne Pathog Dis 2021;19:441-447. [PMID: 34936494 PMCID: PMC9297326 DOI: 10.1089/fpd.2021.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
164
Kajitani R, Noguchi H, Gotoh Y, Ogura Y, Yoshimura D, Okuno M, Toyoda A, Kuwahara T, Hayashi T, Itoh T. MetaPlatanus: a metagenome assembler that combines long-range sequence links and species-specific features. Nucleic Acids Res 2021;49:e130. [PMID: 34570223 PMCID: PMC8682757 DOI: 10.1093/nar/gkab831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 12/27/2022]  Open
165
Liu G, Li P, Hou L, Niu Q, Pu G, Wang B, Du T, Kim SW, Niu P, Li Q, Huang R. Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs. Front Microbiol 2021;12:746717. [PMID: 34867862 PMCID: PMC8637618 DOI: 10.3389/fmicb.2021.746717] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]  Open
166
Robinson SL, Piel J, Sunagawa S. A roadmap for metagenomic enzyme discovery. Nat Prod Rep 2021;38:1994-2023. [PMID: 34821235 PMCID: PMC8597712 DOI: 10.1039/d1np00006c] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
167
Ortiz-Chura A, Gere J, Marcoppido G, Depetris G, Cravero S, Faverín C, Pinares-Patiño C, Cataldi A, Cerón-Cucchi ME. Dynamics of the ruminal microbial ecosystem, and inhibition of methanogenesis and propiogenesis in response to nitrate feeding to Holstein calves. ACTA ACUST UNITED AC 2021;7:1205-1218. [PMID: 34754962 PMCID: PMC8556761 DOI: 10.1016/j.aninu.2021.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 06/25/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022]
168
Ma T, McAllister TA, Guan LL. A review of the resistome within the digestive tract of livestock. J Anim Sci Biotechnol 2021;12:121. [PMID: 34763729 PMCID: PMC8588621 DOI: 10.1186/s40104-021-00643-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/07/2021] [Indexed: 12/25/2022]  Open
169
Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity. CONSERVATION 2021. [DOI: 10.3390/conservation1040024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
170
Enrofloxacin Alters Fecal Microbiota and Resistome Irrespective of Its Dose in Calves. Microorganisms 2021;9:microorganisms9102162. [PMID: 34683483 PMCID: PMC8537546 DOI: 10.3390/microorganisms9102162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/07/2021] [Accepted: 10/13/2021] [Indexed: 12/27/2022]  Open
171
McDaniel EA, Wahl SA, Ishii S, Pinto A, Ziels R, Nielsen PH, McMahon KD, Williams RBH. Prospects for multi-omics in the microbial ecology of water engineering. WATER RESEARCH 2021;205:117608. [PMID: 34555741 DOI: 10.1016/j.watres.2021.117608] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/20/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
172
Kwon MJ, Tripathi BM, Göckede M, Shin SC, Myeong NR, Lee YK, Kim M. Disproportionate microbial responses to decadal drainage on a Siberian floodplain. GLOBAL CHANGE BIOLOGY 2021;27:5124-5140. [PMID: 34216067 DOI: 10.1111/gcb.15785] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
173
Asselstine V, Lam S, Miglior F, Brito LF, Sweett H, Guan L, Waters SM, Plastow G, Cánovas A. The potential for mitigation of methane emissions in ruminants through the application of metagenomics, metabolomics, and other -OMICS technologies. J Anim Sci 2021;99:6377879. [PMID: 34586400 PMCID: PMC8480417 DOI: 10.1093/jas/skab193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022]  Open
174
Adoption of Climate Smart Agriculture by Communal Livestock Farmers in South Africa. SUSTAINABILITY 2021. [DOI: 10.3390/su131810468] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
175
Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns. Proc Natl Acad Sci U S A 2021;118:2016810118. [PMID: 33723043 PMCID: PMC8000110 DOI: 10.1073/pnas.2016810118] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
176
Kayani MUR, Huang W, Feng R, Chen L. Genome-resolved metagenomics using environmental and clinical samples. Brief Bioinform 2021;22:bbab030. [PMID: 33758906 PMCID: PMC8425419 DOI: 10.1093/bib/bbab030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/29/2020] [Accepted: 01/20/2021] [Indexed: 12/25/2022]  Open
177
Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg. mSystems 2021;6:e0072921. [PMID: 34427525 PMCID: PMC8409728 DOI: 10.1128/msystems.00729-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
178
Effects of Age, Diet CP, NDF, EE, and Starch on the Rumen Bacteria Community and Function in Dairy Cattle. Microorganisms 2021;9:microorganisms9081788. [PMID: 34442867 PMCID: PMC8400643 DOI: 10.3390/microorganisms9081788] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 01/22/2023]  Open
179
Ayling M, Clark MD, Leggett RM. New approaches for metagenome assembly with short reads. Brief Bioinform 2021;21:584-594. [PMID: 30815668 PMCID: PMC7299287 DOI: 10.1093/bib/bbz020] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]  Open
180
Metagenome-Assembled Genomes Contribute to Unraveling of the Microbiome of Cocoa Fermentation. Appl Environ Microbiol 2021;87:e0058421. [PMID: 34105982 DOI: 10.1128/aem.00584-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
181
Yuan H, Wang X, Lin TY, Kim J, Liu WT. Disentangling the syntrophic electron transfer mechanisms of Candidatus geobacter eutrophica through electrochemical stimulation and machine learning. Sci Rep 2021;11:15140. [PMID: 34302023 PMCID: PMC8302695 DOI: 10.1038/s41598-021-94628-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023]  Open
182
Xu Z, Dixon JR. Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies. Brief Funct Genomics 2021;19:139-150. [PMID: 31875884 DOI: 10.1093/bfgp/elz026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/06/2019] [Accepted: 09/15/2019] [Indexed: 12/22/2022]  Open
183
Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories. Vet Sci 2021;8:vetsci8070138. [PMID: 34357930 PMCID: PMC8310016 DOI: 10.3390/vetsci8070138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/02/2021] [Accepted: 07/14/2021] [Indexed: 12/29/2022]  Open
184
Sánchez-Reyes A, Bretón-Deval L, Mangelson H, Salinas-Peralta I, Sanchez-Flores A. Hi-C deconvolution of a textile dye-related microbiome reveals novel taxonomic landscapes and links phenotypic potential to individual genomes. Int Microbiol 2021;25:99-110. [PMID: 34269948 DOI: 10.1007/s10123-021-00189-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/20/2021] [Accepted: 06/27/2021] [Indexed: 12/12/2022]
185
Effects of rumen-protected methionine and lysine supplementation on milk yields and components, rumen fermentation, and the rumen microbiome in lactating yaks (Bos grunniens). Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2021.114972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
186
Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics. Commun Biol 2021;4:818. [PMID: 34188189 PMCID: PMC8241843 DOI: 10.1038/s42003-021-02331-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/07/2021] [Indexed: 11/17/2022]  Open
187
Xie F, Jin W, Si H, Yuan Y, Tao Y, Liu J, Wang X, Yang C, Li Q, Yan X, Lin L, Jiang Q, Zhang L, Guo C, Greening C, Heller R, Guan LL, Pope PB, Tan Z, Zhu W, Wang M, Qiu Q, Li Z, Mao S. An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants. MICROBIOME 2021;9:137. [PMID: 34118976 PMCID: PMC8199421 DOI: 10.1186/s40168-021-01078-x] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/15/2021] [Indexed: 05/20/2023]
188
Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife 2021;10:64325. [PMID: 34114561 PMCID: PMC8241443 DOI: 10.7554/elife.64325] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022]  Open
189
Han X, Lei X, Yang X, Shen J, Zheng L, Jin C, Cao Y, Yao J. A Metagenomic Insight Into the Hindgut Microbiota and Their Metabolites for Dairy Goats Fed Different Rumen Degradable Starch. Front Microbiol 2021;12:651631. [PMID: 34163442 PMCID: PMC8216219 DOI: 10.3389/fmicb.2021.651631] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022]  Open
190
Cheng M, Zhang X, Guo Z, Lv P, Xiong R, Wang Z, Zhou Z, Zhang M. Pd-promoting reduction of zinc salt to PdZn alloy catalyst for the hydrogenation of nitrothioanisole. J Colloid Interface Sci 2021;602:459-468. [PMID: 34144303 DOI: 10.1016/j.jcis.2021.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
191
Li Y, Jin Y, Zhang J, Pan H, Wu L, Liu D, Liu J, Hu J, Shen J. Recovery of human gut microbiota genomes with third-generation sequencing. Cell Death Dis 2021;12:569. [PMID: 34078878 PMCID: PMC8172872 DOI: 10.1038/s41419-021-03829-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/26/2022]
192
Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, Clavel T. Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria. ISME COMMUNICATIONS 2021;1:16. [PMID: 36732617 PMCID: PMC9723785 DOI: 10.1038/s43705-021-00017-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/21/2021] [Accepted: 05/04/2021] [Indexed: 02/05/2023]
193
Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria. mSystems 2021;6:6/3/e01300-20. [PMID: 34006629 PMCID: PMC8269260 DOI: 10.1128/msystems.01300-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
194
Hoque MN, Rahman MS, Ahmed R, Hossain MS, Islam MS, Islam T, Hossain MA, Siddiki AZ. Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases. GENE REPORTS 2021;23:101200. [PMID: 33977168 PMCID: PMC8102076 DOI: 10.1016/j.genrep.2021.101200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/03/2021] [Indexed: 12/11/2022]
195
Liu YX, Qin Y, Chen T, Lu M, Qian X, Guo X, Bai Y. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell 2021;12:315-330. [PMID: 32394199 PMCID: PMC8106563 DOI: 10.1007/s13238-020-00724-8] [Citation(s) in RCA: 413] [Impact Index Per Article: 103.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/10/2020] [Indexed: 12/22/2022]  Open
196
Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data. Nat Protoc 2021;16:2520-2541. [PMID: 33864056 DOI: 10.1038/s41596-021-00508-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/12/2021] [Indexed: 02/02/2023]
197
Hinsu AT, Tulsani NJ, Panchal KJ, Pandit RJ, Jyotsana B, Dafale NA, Patil NV, Purohit HJ, Joshi CG, Jakhesara SJ. Characterizing rumen microbiota and CAZyme profile of Indian dromedary camel (Camelus dromedarius) in response to different roughages. Sci Rep 2021;11:9400. [PMID: 33931716 PMCID: PMC8087840 DOI: 10.1038/s41598-021-88943-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/12/2021] [Indexed: 02/07/2023]  Open
198
Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, Alikhan NF, Baker D, Gharbi K, Hall N, Watson M, Adriaenssens EM, Foster-Nyarko E, Jarju S, Secka A, Antonio M, Oren A, Chaudhuri RR, La Ragione R, Hildebrand F, Pallen MJ. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ 2021;9:e10941. [PMID: 33868800 PMCID: PMC8035907 DOI: 10.7717/peerj.10941] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/22/2021] [Indexed: 12/27/2022]  Open
199
Gharechahi J, Vahidi MF, Bahram M, Han JL, Ding XZ, Salekdeh GH. Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen. THE ISME JOURNAL 2021;15:1108-1120. [PMID: 33262428 PMCID: PMC8114923 DOI: 10.1038/s41396-020-00837-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 02/08/2023]
200
Nayfach S, Roux S, Seshadri R, Udwary D, Varghese N, Schulz F, Wu D, Paez-Espino D, Chen IM, Huntemann M, Palaniappan K, Ladau J, Mukherjee S, Reddy TBK, Nielsen T, Kirton E, Faria JP, Edirisinghe JN, Henry CS, Jungbluth SP, Chivian D, Dehal P, Wood-Charlson EM, Arkin AP, Tringe SG, Visel A, Woyke T, Mouncey NJ, Ivanova NN, Kyrpides NC, Eloe-Fadrosh EA. A genomic catalog of Earth's microbiomes. Nat Biotechnol 2021;39:499-509. [PMID: 33169036 PMCID: PMC8041624 DOI: 10.1038/s41587-020-0718-6] [Citation(s) in RCA: 450] [Impact Index Per Article: 112.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 09/28/2020] [Indexed: 01/02/2023]
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