Ahmed W, Payyappat S, Cassidy M, Besley C (2019) A duplex PCR assay for the simultaneous quantification of Bacteroides HF183 and crAssphage CPQ_056 marker genes in untreated sewage and stormwater. Environ Int 126:252–259. https://doi.org/10.1016/j.envint.2019.01.035
Article CAS PubMed Google Scholar
Bae M, Cassilly CD, Liu X, Park SM, Tusi BK, Chen X, Kwon J, Filipčík P, Bolze AS, Liu Z, Vlamakis H, Graham DB, Buhrlage SJ, Xavier RJ, Clardy J (2022) Akkermansia muciniphila phospholipid induces homeostatic immune responses. Nature 608(7921):168–173. https://doi.org/10.1038/s41586-022-04985-7
Article CAS PubMed PubMed Central Google Scholar
Buchfink B, Xie C, Huson DH (2015) Fast and sensitive protein alignment using DIAMOND. Nat Methods 12(1):59–60. https://doi.org/10.1038/nmeth.3176
Article CAS PubMed Google Scholar
Chen Q, Wu G, Chen H, Li H, Li S, Zhang C, Pang X, Wang L, Zhao L, Shen J (2019) Quantification of human oral and fecal Streptococcus parasanguinis by use of quantitative real-time PCR targeting the groEL gene. Front Microbiol 10:2910. https://doi.org/10.3389/fmicb.2019.02910
Article PubMed PubMed Central Google Scholar
Cheng AG, Ho PY, Aranda-Díaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA (2022) Design, construction, and in vivo augmentation of a complex gut microbiome. Cell 185(19):3617–3636e19. https://doi.org/10.1016/j.cell.2022.08.003
Article CAS PubMed PubMed Central Google Scholar
Chiu CY, Miller SA (2019) Clinical metagenomics. Nat Rev Genet 20(6):341–355. https://doi.org/10.1038/s41576-019-0113-7
Article CAS PubMed PubMed Central Google Scholar
Coker OO, Liu C, Wu WKK, Wong SH, Jia W, Sung JJY, Yu J (2022) Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers. Microbiome 10(1):35. https://doi.org/10.1186/s40168-021-01208-5
Article CAS PubMed PubMed Central Google Scholar
Daybog I, Kolodny O (2023) A computational framework for resolving the microbiome diversity conundrum. Nat Commun 14(1):7977. https://doi.org/10.1038/s41467-023-42768-4
Article CAS PubMed PubMed Central Google Scholar
de Vos WM, Tilg H, Van Hul M, Cani PD (2022) Gut microbiome and health: mechanistic insights. Gut 71(5):1020–1032. https://doi.org/10.1136/gutjnl-2021-326789
Article CAS PubMed Google Scholar
de Wit DF, Hanssen NMJ, Wortelboer K, Herrema H, Rampanelli E, Nieuwdorp M (2023) Evidence for the contribution of the gut microbiome to obesity and its reversal. Sci Transl Med 15(723):eadg2773. https://doi.org/10.1126/scitranslmed.adg2773
Article CAS PubMed Google Scholar
Diao Z, Zhang Y, Chen Y, Han Y, Chang L, Ma Y, Feng L, Huang T, Zhang R, Li J (2023) Assessing the quality of metagenomic next-generation sequencing for pathogen detection in lower respiratory infections. Clin Chem 69(9):1038–1049. https://doi.org/10.1093/clinchem/hvad072
Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ (2017) Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun 8(1):1784. https://doi.org/10.1038/s41467-017-01973-8
Article CAS PubMed PubMed Central Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28(23):3150–3152. https://doi.org/10.1093/bioinformatics/bts565
Article CAS PubMed PubMed Central Google Scholar
Gacesa R, Kurilshikov A, Vich Vila A, Sinha T, Klaassen MAY, Bolte LA, Andreu-Sánchez S, Chen L, Collij V, Hu S, Dekens JAM, Lenters VC, Björk JR, Swarte JC, Swertz MA, Jansen BH, Gelderloos-Arends J, Jankipersadsing S, Hofker M, Vermeulen RCH, Sanna S, Harmsen HJM, Wijmenga C, Fu J, Zhernakova A, Weersma RK (2022) Environmental factors shaping the gut microbiome in a Dutch population. Nature 604(7907):732–739. https://doi.org/10.1038/s41586-022-04567-7
Article CAS PubMed Google Scholar
Gautam A, Zeng W, Huson DH, Alkan C (2023) MeganServer: facilitating interactive access to metagenomic data on a server. Bioinformatics 39(3). https://doi.org/10.1093/bioinformatics/btad105
Gray L, Hasebe K, O’Hely M, Ponsonby AL, Vuillermin P, Collier F (2019) Rapid PCR identification of Prevotella copri in an Australian cohort of pregnant women. J Dev Orig Health Dis 11(3):228–234. https://doi.org/10.1017/s2040174419000849
Gui Q, Li H, Wang A, Zhao X, Tan Z, Chen L, Xu K, Xiao C (2020) The association between gut butyrate-producing bacteria and non-small-cell lung cancer. J Clin Lab Anal 34(8):e23318. https://doi.org/10.1002/jcla.23318
Article CAS PubMed PubMed Central Google Scholar
Hasan MR, Sundararaju S, Tang P, Tsui KM, Lopez AP, Janahi M, Tan R, Tilley P (2020) A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting. Sci Rep 10(1):11194. https://doi.org/10.1038/s41598-020-68159-z
Article CAS PubMed PubMed Central Google Scholar
Hou K, Wu Z, Chen X, Wang J, Zhang D, Xiao C, Zhu D, Koya JB, Wei L, Li J, Chen ZS (2022) Microbiota in health and diseases. Signal Transduct Target Ther 7(1):135. https://doi.org/10.1038/s41392-022-00974-4
Article PubMed PubMed Central Google Scholar
Huang Q, Chen D, Du C, Liu Q, Lin S, Liang L, Xu Y, Liao Y, Li Q (2022) Highly multiplex PCR assays by coupling the 5’-flap endonuclease activity of taq DNA polymerase and molecular beacon reporters. Proc Natl Acad Sci USA 119(9). https://doi.org/10.1073/pnas.2110672119
Kurina I, Popenko A, Klimenko N, Koshechkin S, Chuprikova L, Filipenko M, Tyakht A, Alexeev D (2020) Development of qPCR platform with probes for quantifying prevalent and biomedically relevant human gut microbial taxa. Mol Cell Probes 52:101570. https://doi.org/10.1016/j.mcp.2020.101570
Article CAS PubMed PubMed Central Google Scholar
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. https://doi.org/10.1038/nmeth.1923
Article CAS PubMed PubMed Central Google Scholar
Laue H, Smits THM, Schumacher UK, Claros MC, Hartemink R, Cook AM (2006) Identification of Bilophila wadsworthia by specific PCR which targets the taurine:pyruvate aminotransferase gene. FEMS Microbiol Lett 261(1):74–79. https://doi.org/10.1111/j.1574-6968.2006.00335.x
Article CAS PubMed Google Scholar
Lawal SA, Voisin A, Olof H, Bording-Jorgensen M, Armstrong H (2023) Diversity of the microbiota communities found in the various regions of the intestinal tract in healthy individuals and inflammatory bowel diseases. Front Immunol 14:1242242. https://doi.org/10.3389/fimmu.2023.1242242
Article CAS PubMed PubMed Central Google Scholar
Li D, Luo R, Liu C, Leung C, Ting H, Sadakane K, Yamashita H, Lam TW (2016) MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods 102:3–11. https://doi.org/10.1016/j.ymeth.2016.02.020
Article CAS PubMed Google Scholar
Li Y, Shao F, Zheng S, Tan Z, He Y (2020) Alteration of Streptococcus salivarius in buccal mucosa of oral lichen planus and controlled clinical trial in OLP treatment. Probiotics Antimicrob Proteins 12(4):1340–1348. https://doi.org/10.1007/s12602-020-09664-5
Article CAS PubMed Google Scholar
Lim HJ, Lee EH, Yoon Y, Chua B, Son A (2016) Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 120(2):379–387. https://doi.org/10.1111/jam.13011
Comments (0)