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For: Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. Elife 2021;10:e65088. [PMID: 33944776 DOI: 10.7554/eLife.65088] [Cited by in Crossref: 17] [Cited by in F6Publishing: 18] [Article Influence: 17.0] [Reference Citation Analysis]
Number Citing Articles
1 You X, Dadwal UC, Lenburg ME, Kacena MA, Charles JF, Rawls JF. Murine Gut Microbiome Meta-analysis Reveals Alterations in Carbohydrate Metabolism in Response to Aging. mSystems. [DOI: 10.1128/msystems.01248-21] [Reference Citation Analysis]
2 Moroishi Y, Gui J, Nadeau KC, Morrison HG, Madan J, Karagas MR. A prospective study of the infant gut microbiome in relation to vaccine response. Pediatr Res 2022. [PMID: 35717483 DOI: 10.1038/s41390-022-02154-0] [Reference Citation Analysis]
3 Orsso CE, Peng Y, Deehan EC, Tan Q, Field CJ, Madsen KL, Walter J, Prado CM, Tun HM, Haqq AM. Composition and Functions of the Gut Microbiome in Pediatric Obesity: Relationships with Markers of Insulin Resistance. Microorganisms 2021;9:1490. [PMID: 34361925 DOI: 10.3390/microorganisms9071490] [Reference Citation Analysis]
4 Lee KA, Thomas AM, Bolte LA, Björk JR, de Ruijter LK, Armanini F, Asnicar F, Blanco-Miguez A, Board R, Calbet-Llopart N, Derosa L, Dhomen N, Brooks K, Harland M, Harries M, Leeming ER, Lorigan P, Manghi P, Marais R, Newton-Bishop J, Nezi L, Pinto F, Potrony M, Puig S, Serra-Bellver P, Shaw HM, Tamburini S, Valpione S, Vijay A, Waldron L, Zitvogel L, Zolfo M, de Vries EGE, Nathan P, Fehrmann RSN, Bataille V, Hospers GAP, Spector TD, Weersma RK, Segata N. Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma. Nat Med 2022;28:535-44. [PMID: 35228751 DOI: 10.1038/s41591-022-01695-5] [Cited by in Crossref: 10] [Cited by in F6Publishing: 4] [Article Influence: 10.0] [Reference Citation Analysis]
5 Breusing C, Genetti M, Russell SL, Corbett-Detig RB, Beinart RA. Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses. Proc Natl Acad Sci U S A 2022;119:e2115608119. [PMID: 35349333 DOI: 10.1073/pnas.2115608119] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
6 De Filippis F, Paparo L, Nocerino R, Della Gatta G, Carucci L, Russo R, Pasolli E, Ercolini D, Berni Canani R. Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance. Nat Commun 2021;12:5958. [PMID: 34645820 DOI: 10.1038/s41467-021-26266-z] [Reference Citation Analysis]
7 Gwang Song J, Yu M, Lee B, Lee J, Hwang S, Na D, Wook Kim H. Analysis methods for the gut microbiome in neuropsychiatric and neurodegenerative disorders. Computational and Structural Biotechnology Journal 2022. [DOI: 10.1016/j.csbj.2022.02.024] [Reference Citation Analysis]
8 Tomasi M, Dalsass M, Beghini F, Zanella I, Caproni E, Fantappiè L, Gagliardi A, Irene C, König E, Frattini L, Masetti G, Isaac SJ, Armanini F, Cumbo F, Blanco-Míguez A, Grandi A, Segata N, Grandi G. Commensal Bifidobacterium Strains Enhance the Efficacy of Neo-Epitope Based Cancer Vaccines. Vaccines (Basel) 2021;9:1356. [PMID: 34835287 DOI: 10.3390/vaccines9111356] [Reference Citation Analysis]
9 Bommana S, Richards G, Kama M, Kodimerla R, Jijakli K, Read TD, Dean D. Metagenomic Shotgun Sequencing of Endocervical, Vaginal, and Rectal Samples among Fijian Women with and without Chlamydia trachomatis Reveals Disparate Microbial Populations and Function across Anatomic Sites: a Pilot Study. Microbiol Spectr 2022;:e0010522. [PMID: 35579443 DOI: 10.1128/spectrum.00105-22] [Reference Citation Analysis]
10 Wang Z, Bai Y, Pi Y, Gerrits WJJ, de Vries S, Shang L, Tao S, Zhang S, Han D, Zhu Z, Wang J. Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs. Microbiome 2021;9:227. [PMID: 34802456 DOI: 10.1186/s40168-021-01175-x] [Reference Citation Analysis]
11 Mathieu A, Leclercq M, Sanabria M, Perin O, Droit A. Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation. Front Microbiol 2022;13:811495. [PMID: 35359727 DOI: 10.3389/fmicb.2022.811495] [Reference Citation Analysis]
12 Stege PB, Hordijk J, Shetty SA, Visser M, Viveen MC, Rogers MRC, Gijsbers E, Dierikx CM, van der Plaats RQJ, van Duijkeren E, Franz E, Willems RJL, Fuentes S, Paganelli FL. Impact of long-term dietary habits on the human gut resistome in the Dutch population. Sci Rep 2022;12:1892. [PMID: 35115599 DOI: 10.1038/s41598-022-05817-4] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
13 Raman M, Ma C, Taylor LM, Dieleman LA, Gkoutos GV, Vallance JK, McCoy KD, Lewis I, Jijon H, McKay DM, Mutch DM, Barkema HW, Gibson D, Rauch M, Ghosh S. Crohn's disease therapeutic dietary intervention (CD-TDI): study protocol for a randomised controlled trial. BMJ Open Gastroenterol 2022;9:e000841. [PMID: 35046093 DOI: 10.1136/bmjgast-2021-000841] [Reference Citation Analysis]
14 Jin S, Wetzel D, Schirmer M. Deciphering mechanisms and implications of bacterial translocation in human health and disease. Curr Opin Microbiol 2022;67:102147. [PMID: 35461008 DOI: 10.1016/j.mib.2022.102147] [Reference Citation Analysis]
15 Goussarov G, Mysara M, Vandamme P, Van Houdt R. Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. Microbiologyopen 2022;11:e1298. [PMID: 35765182 DOI: 10.1002/mbo3.1298] [Reference Citation Analysis]
16 Bonham K, Kayisire A, Luo A, Klepac-ceraj V. Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data. JOSS 2021;6:3876. [DOI: 10.21105/joss.03876] [Reference Citation Analysis]
17 Piredda I, Bertoldi L, Benvenuto G, Palmas B, Pedditzi A, Pintore P, Chisu V. First Isolation and Molecular Typing of Pathogenic and Intermediate Leptospira Species from Urine of Symptomatic Dogs. Vet Sci 2021;8:304. [PMID: 34941830 DOI: 10.3390/vetsci8120304] [Reference Citation Analysis]
18 Rubin IMC, Mollerup S, Broholm C, Knudsen SB, Baker A, Helms M, Holm MKA, Kallemose T, Westh H, Dahl Knudsen J, Pinholt M, Petersen AM. No Effect of Lactobacillus rhamnosus GG on Eradication of Colonization by Vancomycin-Resistant Enterococcus faecium or Microbiome Diversity in Hospitalized Adult Patients. Microbiol Spectr 2022;10:e0234821. [PMID: 35475684 DOI: 10.1128/spectrum.02348-21] [Reference Citation Analysis]
19 Dizman N, Meza L, Bergerot P, Alcantara M, Dorff T, Lyou Y, Frankel P, Cui Y, Mira V, Llamas M, Hsu J, Zengin Z, Salgia N, Salgia S, Malhotra J, Chawla N, Chehrazi-Raffle A, Muddasani R, Gillece J, Reining L, Trent J, Takahashi M, Oka K, Higashi S, Kortylewski M, Highlander SK, Pal SK. Nivolumab plus ipilimumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial. Nat Med 2022. [PMID: 35228755 DOI: 10.1038/s41591-022-01694-6] [Cited by in Crossref: 12] [Cited by in F6Publishing: 10] [Article Influence: 12.0] [Reference Citation Analysis]
20 Wang Z, Usyk M, Vázquez-Baeza Y, Chen GC, Isasi CR, Williams-Nguyen JS, Hua S, McDonald D, Thyagarajan B, Daviglus ML, Cai J, North KE, Wang T, Knight R, Burk RD, Kaplan RC, Qi Q. Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity. Genome Biol 2021;22:336. [PMID: 34893089 DOI: 10.1186/s13059-021-02559-w] [Reference Citation Analysis]
21 Cerezo-Cortés MI, Rodríguez-Castillo JG, Mata-Espinosa DA, Bini EI, Barrios-Payan J, Zatarain-Barrón ZL, Anzola JM, Cornejo-Granados F, Ochoa-Leyva A, Del Portillo P, Murcia MI, Hernández-Pando R. Close Related Drug-Resistance Beijing Isolates of Mycobacterium tuberculosis Reveal a Different Transcriptomic Signature in a Murine Disease Progression Model. Int J Mol Sci 2022;23:5157. [PMID: 35563545 DOI: 10.3390/ijms23095157] [Reference Citation Analysis]
22 Clavel T, Horz HP, Segata N, Vehreschild M. Next steps after 15 stimulating years of human gut microbiome research. Microb Biotechnol 2022;15:164-75. [PMID: 34818454 DOI: 10.1111/1751-7915.13970] [Reference Citation Analysis]
23 Amar Y, Lagkouvardos I, Silva RL, Ishola OA, Foesel BU, Kublik S, Schöler A, Niedermeier S, Bleuel R, Zink A, Neuhaus K, Schloter M, Biedermann T, Köberle M. Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA. Microbiome 2021;9:123. [PMID: 34039428 DOI: 10.1186/s40168-021-01067-0] [Reference Citation Analysis]
24 Ghazi AR, Münch PC, Chen D, Jensen J, Huttenhower C. Strain identification and quantitative analysis in microbial communities. Journal of Molecular Biology 2022. [DOI: 10.1016/j.jmb.2022.167582] [Reference Citation Analysis]
25 Zhou H, Beltrán JF, Brito IL. Host-microbiome protein-protein interactions capture disease-relevant pathways. Genome Biol 2022;23:72. [PMID: 35246229 DOI: 10.1186/s13059-022-02643-9] [Reference Citation Analysis]
26 Tang X, Shang J, Sun Y. RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data. Brief Bioinform 2022:bbac011. [PMID: 35136930 DOI: 10.1093/bib/bbac011] [Reference Citation Analysis]
27 Zhou Z, Tran PQ, Breister AM, Liu Y, Kieft K, Cowley ES, Karaoz U, Anantharaman K. METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. Microbiome 2022;10:33. [PMID: 35172890 DOI: 10.1186/s40168-021-01213-8] [Cited by in Crossref: 10] [Cited by in F6Publishing: 3] [Article Influence: 10.0] [Reference Citation Analysis]
28 You L, Yang C, Jin H, Kwok L, Sun Z, Zhang H. Metagenomic features of traditional fermented milk products. LWT 2022;155:112945. [DOI: 10.1016/j.lwt.2021.112945] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
29 Sun Y, Snow D, Walia H, Li X. Transmission Routes of the Microbiome and Resistome from Manure to Soil and Lettuce. Environ Sci Technol 2021. [PMID: 34323079 DOI: 10.1021/acs.est.1c02985] [Cited by in Crossref: 2] [Article Influence: 2.0] [Reference Citation Analysis]
30 Li B, Li X, Wang B, Yan T. A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure. Appl Environ Microbiol 2022;:e0255421. [PMID: 35285243 DOI: 10.1128/aem.02554-21] [Reference Citation Analysis]
31 Hernandez-Baixauli J, Abasolo N, Palacios-Jordan H, Foguet-Romero E, Suñol D, Galofré M, Caimari A, Baselga-Escudero L, Del Bas JM, Mulero M. Imbalances in TCA, Short Fatty Acids and One-Carbon Metabolisms as Important Features of Homeostatic Disruption Evidenced by a Multi-Omics Integrative Approach of LPS-Induced Chronic Inflammation in Male Wistar Rats. Int J Mol Sci 2022;23:2563. [PMID: 35269702 DOI: 10.3390/ijms23052563] [Reference Citation Analysis]
32 Yarlagadda K, Razik I, Malhi RS, Carter GG. Social convergence of gut microbiomes in vampire bats. Biol Lett 2021;17:20210389. [PMID: 34727703 DOI: 10.1098/rsbl.2021.0389] [Reference Citation Analysis]
33 Testerman T, Li Z, Galuppo B, Graf J, Santoro N. Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth. Hepatol Commun 2022. [PMID: 35344283 DOI: 10.1002/hep4.1944] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
34 Czech L, Stamatakis A, Dunthorn M, Barbera P. Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade. Front Bioinform 2022;2:871393. [DOI: 10.3389/fbinf.2022.871393] [Reference Citation Analysis]
35 Tourlousse DM, Narita K, Miura T, Ohashi A, Matsuda M, Ohyama Y, Shimamura M, Furukawa M, Kasahara K, Kameyama K, Saito S, Goto M, Shimizu R, Mishima R, Nakayama J, Hosomi K, Kunisawa J, Terauchi J, Sekiguchi Y, Kawasaki H. Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements. Microbiol Spectr 2022;:e0191521. [PMID: 35234490 DOI: 10.1128/spectrum.01915-21] [Reference Citation Analysis]
36 Wu F, Liu YZ, Ling B. MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data. Brief Bioinform 2022:bbac111. [PMID: 35380623 DOI: 10.1093/bib/bbac111] [Reference Citation Analysis]
37 Yen S, Johnson JS. Metagenomics: a path to understanding the gut microbiome. Mamm Genome 2021;32:282-96. [PMID: 34259891 DOI: 10.1007/s00335-021-09889-x] [Reference Citation Analysis]
38 Mäklin T, Kallonen T, Alanko J, Samuelsen Ø, Hegstad K, Mäkinen V, Corander J, Heinz E, Honkela A. Bacterial genomic epidemiology with mixed samples. Microb Genom 2021;7. [PMID: 34779765 DOI: 10.1099/mgen.0.000691] [Reference Citation Analysis]
39 Jiao J, Yang M, Zhang T, Zhang Y, Yang M, Li M, Liu C, Song S, Bai T, Song C, Wang M, Pang H, Feng J, Zheng X. A sensitive visual method for onsite detection of quarantine pathogenic bacteria from horticultural crops using an LbCas12a variant system. J Hazard Mater 2021;426:128038. [PMID: 34953258 DOI: 10.1016/j.jhazmat.2021.128038] [Reference Citation Analysis]
40 New FN, Baer BR, Clark AG, Wells MT, Brito IL. Collective effects of human genomic variation on microbiome function. Sci Rep 2022;12:3839. [PMID: 35264618 DOI: 10.1038/s41598-022-07632-3] [Reference Citation Analysis]
41 Hua H, Meydan C, Afshin EE, Lili LN, D’adamo CR, Rickard N, Dudley JT, Price ND, Zhang B, Mason CE. A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling. Front Immunol 2022;13:889702. [DOI: 10.3389/fimmu.2022.889702] [Reference Citation Analysis]
42 Skoufos G, Almodaresi F, Zakeri M, Paulson JN, Patro R, Hatzigeorgiou AG, Vlachos IS. AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite. Genome Biol 2022;23. [DOI: 10.1186/s13059-022-02610-4] [Reference Citation Analysis]
43 Armstrong AJS, Parmar V, Blaser MJ. Assessing saliva microbiome collection and processing methods. NPJ Biofilms Microbiomes 2021;7:81. [PMID: 34795298 DOI: 10.1038/s41522-021-00254-z] [Reference Citation Analysis]
44 Han M, Zhang N, Mao Y, Huang B, Ren M, Peng Z, Bai Z, Chen L, Liu Y, Wang S, Huang S, Cheng Z. The Potential of Gut Microbiota Metabolic Capability to Detect Drug Response in Rheumatoid Arthritis Patients. Front Microbiol 2022;13:839015. [DOI: 10.3389/fmicb.2022.839015] [Reference Citation Analysis]
45 Hadzega D, Minarik G, Karaba M, Kalavska K, Benca J, Ciernikova S, Sedlackova T, Nemcova P, Bohac M, Pindak D, Klucar L, Mego M. Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq. Int J Mol Sci 2021;22:9058. [PMID: 34445764 DOI: 10.3390/ijms22169058] [Reference Citation Analysis]
46 Andrews MC, Duong CPM, Gopalakrishnan V, Iebba V, Chen WS, Derosa L, Khan MAW, Cogdill AP, White MG, Wong MC, Ferrere G, Fluckiger A, Roberti MP, Opolon P, Alou MT, Yonekura S, Roh W, Spencer CN, Curbelo IF, Vence L, Reuben A, Johnson S, Arora R, Morad G, Lastrapes M, Baruch EN, Little L, Gumbs C, Cooper ZA, Prieto PA, Wani K, Lazar AJ, Tetzlaff MT, Hudgens CW, Callahan MK, Adamow M, Postow MA, Ariyan CE, Gaudreau PO, Nezi L, Raoult D, Mihalcioiu C, Elkrief A, Pezo RC, Haydu LE, Simon JM, Tawbi HA, McQuade J, Hwu P, Hwu WJ, Amaria RN, Burton EM, Woodman SE, Watowich S, Diab A, Patel SP, Glitza IC, Wong MK, Zhao L, Zhang J, Ajami NJ, Petrosino J, Jenq RR, Davies MA, Gershenwald JE, Futreal PA, Sharma P, Allison JP, Routy B, Zitvogel L, Wargo JA. Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade. Nat Med 2021;27:1432-41. [PMID: 34239137 DOI: 10.1038/s41591-021-01406-6] [Cited by in Crossref: 2] [Cited by in F6Publishing: 6] [Article Influence: 2.0] [Reference Citation Analysis]
47 Schneeberger PHH, Gueuning M, Welsche S, Hürlimann E, Dommann J, Häberli C, Frey JE, Sayasone S, Keiser J. Different gut microbial communities correlate with efficacy of albendazole-ivermectin against soil-transmitted helminthiases. Nat Commun 2022;13:1063. [PMID: 35217670 DOI: 10.1038/s41467-022-28658-1] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
48 Uranga C, Nelson KE, Edlund A, Baker JL. Tetramic Acids Mutanocyclin and Reutericyclin A, Produced by Streptococcus mutans Strain B04Sm5 Modulate the Ecology of an in vitro Oral Biofilm. Front Oral Health 2021;2:796140. [PMID: 35048077 DOI: 10.3389/froh.2021.796140] [Reference Citation Analysis]
49 Sarhan MS, Lehmkuhl A, Straub R, Tett A, Wieland G, Francken M, Zink A, Maixner F. Ancient DNA diffuses from human bones to cave stones. iScience 2021;24:103397. [PMID: 34988387 DOI: 10.1016/j.isci.2021.103397] [Reference Citation Analysis]
50 Deutsch L, Debevec T, Millet GP, Osredkar D, Opara S, Šket R, Murovec B, Mramor M, Plavec J, Stres B. Urine and Fecal 1H-NMR Metabolomes Differ Significantly between Pre-Term and Full-Term Born Physically Fit Healthy Adult Males. Metabolites 2022;12:536. [PMID: 35736470 DOI: 10.3390/metabo12060536] [Reference Citation Analysis]
51 Liwinski T, Heinemann M, Schramm C. The intestinal and biliary microbiome in autoimmune liver disease-current evidence and concepts. Semin Immunopathol 2022. [PMID: 35536431 DOI: 10.1007/s00281-022-00936-6] [Reference Citation Analysis]
52 Kang Y, Chen S, Chen Y, Tian L, Wu Q, Zheng M, Li Z. Alterations of fecal antibiotic resistome in COVID-19 patients after empirical antibiotic exposure. Int J Hyg Environ Health 2021;240:113882. [PMID: 34915282 DOI: 10.1016/j.ijheh.2021.113882] [Cited by in Crossref: 4] [Cited by in F6Publishing: 3] [Article Influence: 4.0] [Reference Citation Analysis]
53 Piredda I, Sechi S, Cocco R, Bertoldi L, Palmas B, Chisu V. Isolation of Leptospira interrogans Serovar Canicola in a Vaccinated Dog without Clinical Symptoms. Pathogens 2022;11:406. [DOI: 10.3390/pathogens11040406] [Reference Citation Analysis]
54 Khieu V, Ananta P, Kaewprasert O, Laohaviroj M, Namwat W, Faksri K. Whole-Genome Sequencing Analysis to Identify Infection with Multiple Species of Nontuberculous Mycobacteria. Pathogens 2021;10:879. [PMID: 34358029 DOI: 10.3390/pathogens10070879] [Reference Citation Analysis]
55 Xu X, Zhang W, Guo M, Xiao C, Fu Z, Yu S, Jiang L, Wang S, Ling Y, Liu F, Tan Y, Chen S. Integrated analysis of gut microbiome and host immune responses in COVID-19. Front Med 2022. [PMID: 35258762 DOI: 10.1007/s11684-022-0921-6] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
56 Hu Y, Irinyi L, Hoang MTV, Eenjes T, Graetz A, Stone EA, Meyer W, Schwessinger B, Rathjen JP, Gillian Turgeon B. Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data. mBio. [DOI: 10.1128/mbio.02444-21] [Reference Citation Analysis]
57 Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A. Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts. Cell Rep 2022;38:110204. [PMID: 35021085 DOI: 10.1016/j.celrep.2021.110204] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
58 Phan J, Nair D, Jain S, Montagne T, Flores DV, Nguyen A, Dietsche S, Gombar S, Cotter P. Alterations in Gut Microbiome Composition and Function in Irritable Bowel Syndrome and Increased Probiotic Abundance with Daily Supplementation. mSystems 2021;:e0121521. [PMID: 34726487 DOI: 10.1128/mSystems.01215-21] [Reference Citation Analysis]
59 Tudela H, Claus SP, Saleh M. Next Generation Microbiome Research: Identification of Keystone Species in the Metabolic Regulation of Host-Gut Microbiota Interplay. Front Cell Dev Biol 2021;9:719072. [PMID: 34540837 DOI: 10.3389/fcell.2021.719072] [Reference Citation Analysis]
60 Chen J, Sun L, Liu X, Yu Q, Qin K, Cao X, Gu J. Metagenomic Assessment of the Pathogenic Risk of Microorganisms in Sputum of Postoperative Patients With Pulmonary Infection. Front Cell Infect Microbiol 2022;12:855839. [DOI: 10.3389/fcimb.2022.855839] [Reference Citation Analysis]
61 Lewis CR, Bonham KS, McCann SH, Volpe AR, D'Sa V, Naymik M, De Both MD, Huentelman MJ, Lemery-Chalfant K, Highlander SK, Deoni SCL, Klepac-Ceraj V. Family SES Is Associated with the Gut Microbiome in Infants and Children. Microorganisms 2021;9:1608. [PMID: 34442687 DOI: 10.3390/microorganisms9081608] [Reference Citation Analysis]
62 Lewin GR, Stocke KS, Lamont RJ, Whiteley M. A quantitative framework reveals traditional laboratory growth is a highly accurate model of human oral infection. Proc Natl Acad Sci U S A 2022;119:e2116637119. [PMID: 34992142 DOI: 10.1073/pnas.2116637119] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
63 Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN. Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe 2021;29:1294-1304.e4. [PMID: 34297922 DOI: 10.1016/j.chom.2021.06.019] [Cited by in Crossref: 2] [Article Influence: 2.0] [Reference Citation Analysis]
64 Wang K, Gao P, Geng L, Liu C, Zhang J, Shu C. Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line. Microbiome 2022;10:90. [PMID: 35698170 DOI: 10.1186/s40168-022-01291-2] [Reference Citation Analysis]
65 Podlesny D, Arze C, Dörner E, Verma S, Dutta S, Walter J, Fricke WF. Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation. Microbiome 2022;10:53. [PMID: 35337386 DOI: 10.1186/s40168-022-01251-w] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
66 Belstrøm D, Constancias F, Markvart M, Sikora M, Sørensen CE, Givskov M. Transcriptional Activity of Predominant Streptococcus Species at Multiple Oral Sites Associate With Periodontal Status. Front Cell Infect Microbiol 2021;11:752664. [PMID: 34621696 DOI: 10.3389/fcimb.2021.752664] [Reference Citation Analysis]
67 Spekker O, Váradi OA, Szekeres A, Jäger HY, Zink A, Berner M, Pany-Kucera D, Strondl L, Klostermann P, Samu L, Király K, Bereczki Z, Molnár E, Pálfi G, Tihanyi B. A rare case of calvarial tuberculosis from the Avar Age (8th century CE) cemetery of Kaba-Bitózug (Hajdú-Bihar county, Hungary) - Pathogenesis and differential diagnostic aspects. Tuberculosis (Edinb) 2022;135:102226. [PMID: 35759869 DOI: 10.1016/j.tube.2022.102226] [Reference Citation Analysis]
68 Zeybel M, Arif M, Li X, Altay O, Yang H, Shi M, Akyildiz M, Saglam B, Gonenli MG, Yigit B, Ulukan B, Ural D, Shoaie S, Turkez H, Nielsen J, Zhang C, Uhlén M, Borén J, Mardinoglu A. Multiomics Analysis Reveals the Impact of Microbiota on Host Metabolism in Hepatic Steatosis. Adv Sci (Weinh) 2022;9:e2104373. [PMID: 35128832 DOI: 10.1002/advs.202104373] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
69 García-Cazorla Y, Vasconcelos V. Emergent marine toxins risk assessment using molecular and chemical approaches. EFSA J 2022;20:e200422. [PMID: 35634545 DOI: 10.2903/j.efsa.2022.e200422] [Reference Citation Analysis]
70 Chen J, Byun H, Liu R, Jung I, Pu Q, Zhu CY, Tanchoco E, Alavi S, Degnan PH, Ma AT, Roggiani M, Beld J, Goulian M, Hsiao A, Zhu J. A commensal-encoded genotoxin drives restriction of Vibrio cholerae colonization and host gut microbiome remodeling. Proc Natl Acad Sci U S A 2022;119:e2121180119. [DOI: 10.1073/pnas.2121180119] [Cited by in Crossref: 2] [Cited by in F6Publishing: 1] [Article Influence: 2.0] [Reference Citation Analysis]
71 Tong C, Xiao D, Xie L, Yang J, Zhao R, Hao J, Huo Z, Zeng Z, Xiong W. Swine manure facilitates the spread of antibiotic resistome including tigecycline-resistant tet(X) variants to farm workers and receiving environment. Sci Total Environ 2021;808:152157. [PMID: 34871697 DOI: 10.1016/j.scitotenv.2021.152157] [Reference Citation Analysis]
72 Peterson D, Bonham KS, Rowland S, Pattanayak CW, Klepac-Ceraj V; RESONANCE Consortium. Comparative Analysis of 16S rRNA Gene and Metagenome Sequencing in Pediatric Gut Microbiomes. Front Microbiol 2021;12:670336. [PMID: 34335499 DOI: 10.3389/fmicb.2021.670336] [Reference Citation Analysis]
73 Derosa L, Routy B, Thomas AM, Iebba V, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Moro-Sibilot D, Goldwasser F, Silva CAC, Terrisse S, Bonvalet M, Scherpereel A, Pegliasco H, Richard C, Ghiringhelli F, Elkrief A, Desilets A, Blanc-Durand F, Cumbo F, Blanco A, Boidot R, Chevrier S, Daillère R, Kroemer G, Alla L, Pons N, Le Chatelier E, Galleron N, Roume H, Dubuisson A, Bouchard N, Messaoudene M, Drubay D, Deutsch E, Barlesi F, Planchard D, Segata N, Martinez S, Zitvogel L, Soria JC, Besse B. Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer. Nat Med 2022. [PMID: 35115705 DOI: 10.1038/s41591-021-01655-5] [Cited by in Crossref: 15] [Cited by in F6Publishing: 6] [Article Influence: 15.0] [Reference Citation Analysis]
74 Tamburini FB, Maghini D, Oduaran OH, Brewster R, Hulley MR, Sahibdeen V, Norris SA, Tollman S, Kahn K, Wagner RG, Wade AN, Wafawanaka F, Gómez-Olivé FX, Twine R, Lombard Z, Hazelhurst S, Bhatt AS; H3Africa AWI-Gen Collaborative Centre. Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa. Nat Commun 2022;13:926. [PMID: 35194028 DOI: 10.1038/s41467-021-27917-x] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
75 Huus KE, Hoang TT, Creus-Cuadros A, Cirstea M, Vogt SL, Knuff-Janzen K, Sansonetti PJ, Vonaesch P, Finlay BB. Cross-feeding between intestinal pathobionts promotes their overgrowth during undernutrition. Nat Commun 2021;12:6860. [PMID: 34824233 DOI: 10.1038/s41467-021-27191-x] [Reference Citation Analysis]
76 Rey KM, Tam FF, Enns W, Rahim JF, Safari K, Guinto E, Van Rossum T, Brinkman FSL, Choy JC. Dysbiosis of the Female Murine Gut Microbiome Exacerbates Neutrophil-Mediated Vascular Allograft Injury by Affecting Immunoregulation by Acetate. Transplantation 2022. [PMID: 35485447 DOI: 10.1097/TP.0000000000004161] [Reference Citation Analysis]
77 Hallowell HA, Higgins KV, Roberts M, Johnson RM, Bayne J, Maxwell HS, Brandebourg T, Hiltbold Schwartz E. Longitudinal Analysis of the Intestinal Microbiota in the Obese Mangalica Pig Reveals Alterations in Bacteria and Bacteriophage Populations Associated With Changes in Body Composition and Diet. Front Cell Infect Microbiol 2021;11:698657. [PMID: 34737972 DOI: 10.3389/fcimb.2021.698657] [Reference Citation Analysis]
78 Haran JP, Bradley E, Zeamer AL, Cincotta L, Salive MC, Dutta P, Mutaawe S, Anya O, Meza-Segura M, Moormann AM, Ward DV, McCormick BA, Bucci V. Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long COVID. JCI Insight 2021;6:e152346. [PMID: 34403368 DOI: 10.1172/jci.insight.152346] [Reference Citation Analysis]
79 Liu J, Xu Z, Li H, Chen F, Han K, Hu X, Fang Y, Chen D. Metagenomic Approaches Reveal Strain Profiling and Genotyping of Klebsiella pneumoniae from Hospitalized Patients in China. Microbiol Spectr 2022;:e0219021. [PMID: 35319275 DOI: 10.1128/spectrum.02190-21] [Reference Citation Analysis]
80 Robeson MS 2nd, Manna K, Randolph C, Byrum S, Hakkak R. Short-Term Metformin Treatment Enriches Bacteroides dorei in an Obese Liver Steatosis Zucker Rat Model. Front Microbiol 2022;13:834776. [PMID: 35432282 DOI: 10.3389/fmicb.2022.834776] [Reference Citation Analysis]
81 Qi C, Zhou J, Tu H, Tu R, Chang H, Chen J, Li D, Sun J, Yu R. Lactation-dependent vertical transmission of natural probiotics from the mother to the infant gut through breast milk. Food Funct 2021. [PMID: 34889924 DOI: 10.1039/d1fo03131g] [Cited by in Crossref: 2] [Article Influence: 2.0] [Reference Citation Analysis]
82 Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods 2022. [PMID: 35396482 DOI: 10.1038/s41592-022-01431-4] [Cited by in Crossref: 8] [Cited by in F6Publishing: 1] [Article Influence: 8.0] [Reference Citation Analysis]
83 Smith BJ, Li X, Shi ZJ, Abate A, Pollard KS. Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts. Front Bioinform 2022;2:867386. [DOI: 10.3389/fbinf.2022.867386] [Reference Citation Analysis]
84 Bernigaud C, Zakrzewski M, Taylor S, Swe PM, Papenfuss AT, Sriprakash KS, Holt D, Chosidow O, Currie BJ, Fischer K. First Description of the Composition and the Functional Capabilities of the Skin Microbial Community Accompanying Severe Scabies Infestation in Humans. Microorganisms 2021;9:907. [PMID: 33922793 DOI: 10.3390/microorganisms9050907] [Reference Citation Analysis]
85 Lacey KA, Gonzalez S, Yeung F, Putzel G, Podkowik M, Pironti A, Shopsin B, Cadwell K, Torres VJ. Microbiome-Independent Effects of Antibiotics in a Murine Model of Nosocomial Infections. mBio 2022;:e0124022. [PMID: 35612285 DOI: 10.1128/mbio.01240-22] [Cited by in Crossref: 1] [Cited by in F6Publishing: 1] [Article Influence: 1.0] [Reference Citation Analysis]
86 McKee AM, Kirkup BM, Madgwick M, Fowler WJ, Price CA, Dreger SA, Ansorge R, Makin KA, Caim S, Le Gall G, Paveley J, Leclaire C, Dalby M, Alcon-Giner C, Andrusaite A, Feng TY, Di Modica M, Triulzi T, Tagliabue E, Milling SWF, Weilbaecher KN, Rutkowski MR, Korcsmáros T, Hall LJ, Robinson SD. Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumor growth. iScience 2021;24:103012. [PMID: 34522855 DOI: 10.1016/j.isci.2021.103012] [Cited by in Crossref: 1] [Article Influence: 1.0] [Reference Citation Analysis]
87 Ma X, Brinker E, Graff EC, Cao W, Gross AL, Johnson AK, Zhang C, Martin DR, Wang X. Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats. Microbiol Spectr 2022;:e0083722. [PMID: 35467389 DOI: 10.1128/spectrum.00837-22] [Reference Citation Analysis]
88 Hernandez-Baixauli J, Puigbò P, Abasolo N, Palacios-Jordan H, Foguet-Romero E, Suñol D, Galofré M, Caimari A, Baselga-Escudero L, Bas JMD, Mulero M. Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach. Int J Mol Sci 2021;22:12931. [PMID: 34884735 DOI: 10.3390/ijms222312931] [Reference Citation Analysis]