The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems DOI Creative Commons

Jesse R. Willis,

Toni Gabaldón

Microorganisms, Год журнала: 2020, Номер 8(2), С. 308 - 308

Опубликована: Фев. 23, 2020

The human oral cavity is home to an abundant and diverse microbial community (i.e., the microbiome), whose composition roles in health disease have been focus of intense research recent years. Thanks developments sequencing-based approaches, such as 16S ribosomal RNA metabarcoding, whole metagenome shotgun sequencing, or meta-transcriptomics, we now can efficiently explore diversity microbes, even if unculturable. Recent studies charted ecosystems how they change due lifestyle conditions. As progress, there increasing evidence important role microbiome conditions, which are not limited diseases cavity. This, turn, opens new avenues for microbiome-based diagnostics therapeutics that benefit from easy accessibility monitoring manipulation. Yet, many challenges remain ahead. In this review, survey main methodologies currently used highlight major findings enabled by these approaches. Finally, discuss future prospects field.

Язык: Английский

The Human Gut Microbiome: From Association to Modulation DOI Creative Commons
Thomas Schmidt, Jeroen Raes, Peer Bork

и другие.

Cell, Год журнала: 2018, Номер 172(6), С. 1198 - 1215

Опубликована: Март 1, 2018

Язык: Английский

Процитировано

705
Interaction between drugs and the gut microbiome DOI Creative Commons
Rinse K. Weersma, Alexandra Zhernakova, Jingyuan Fu

и другие.

Gut, Год журнала: 2020, Номер 69(8), С. 1510 - 1519

Опубликована: Май 14, 2020

The human gut microbiome is a complex ecosystem that can mediate the interaction of host with their environment. between microbes and commonly used non-antibiotic drugs bidirectional: composition be influenced by drugs, but, vice versa, also influence an individual's response to drug enzymatically transforming drug's structure altering its bioavailability, bioactivity or toxicity (pharmacomicrobiomics). indirectly impact immunotherapy in cancer treatment. In this review we discuss bidirectional interactions describe changes microbiota induced potential clinical consequences summarise how impacts effectiveness role immunotherapy. Understanding metabolises reduces treatment efficacy will unlock possibility modulating improve

Язык: Английский

Процитировано

689
Management of Rheumatoid Arthritis: An Overview DOI Creative Commons
Andrei-Flavius Radu,

Simona Bungău

Cells, Год журнала: 2021, Номер 10(11), С. 2857 - 2857

Опубликована: Окт. 23, 2021

Rheumatoid arthritis (RA) is a multifactorial autoimmune disease of unknown etiology, primarily affecting the joints, then extra-articular manifestations can occur. Due to its complexity, which based on an incompletely elucidated pathophysiological mechanism, good RA management requires multidisciplinary approach. The clinical status patients has improved in recent years due medical advances diagnosis and treatment, that have made it possible reduce activity prevent systemic complications. most promising results were obtained by developing disease-modifying anti-rheumatic drugs (DMARDs), class conventional synthetic, biologic, targeted synthetic belong. Furthermore, ongoing drug development led obtaining molecules with efficacy safety profiles, but further research needed until turns into curable pathology. In present work, we offer comprehensive perspective RA, centralizing existing data provided significant literature, emphasizing importance early accurate associated optimal personalized treatment order achieve better outcomes for patients. addition, this study suggests future perspectives could lead higher profiles lower financial costs.

Язык: Английский

Процитировано

616
A practical guide to amplicon and metagenomic analysis of microbiome data DOI Creative Commons
Yongxin Liu, Yuan Qin, Tong Chen

и другие.

Protein & Cell, Год журнала: 2020, Номер 12(5), С. 315 - 330

Опубликована: Май 11, 2020

Abstract Advances in high-throughput sequencing (HTS) have fostered rapid developments the field of microbiome research, and massive datasets are now being generated. However, diversity software tools complexity analysis pipelines make it difficult to access this field. Here, we systematically summarize advantages limitations methods. Then, recommend specific for amplicon metagenomic analyses, describe commonly-used databases, help researchers select appropriate tools. Furthermore, introduce statistical visualization methods suitable analysis, including alpha- beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, common styles informed choices. Finally, a step-by-step reproducible guide is introduced. We hope review will allow carry out data more effectively quickly order efficiently mine biological significance behind data.

Язык: Английский

Процитировано

613
Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma DOI Creative Commons
Zhigang Ren, Ang Li, Jianwen Jiang

и другие.

Gut, Год журнала: 2018, Номер 68(6), С. 1014 - 1023

Опубликована: Июль 25, 2018

Objective To characterise gut microbiome in patients with hepatocellular carcinoma (HCC) and evaluate the potential of as non-invasive biomarkers for HCC. Design We collected 486 faecal samples from East China, Central China Northwest prospectively finally 419 completed Miseq sequencing. characterised microbiome, identified microbial markers constructed HCC classifier 75 early HCC, 40 cirrhosis healthy controls. validated results 56 controls, 30 45 advanced further verified diagnosis 18 Xinjiang 80 Zhengzhou. Results Faecal diversity was increased to cirrhosis. Phylum Actinobacteria versus Correspondingly, 13 genera including Gemmiger Parabacteroides were enriched Butyrate-producing decreased, while producing-lipopolysaccharide The optimal through a fivefold cross-validation on random forest model achieved an area under curve 80.64% between 105 non-HCC samples. Notably, strong even Importantly, successfully cross-region validation China. Conclusions This study is first report successful establishment Gut microbiota-targeted represent tools

Язык: Английский

Процитировано

592
Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? DOI Creative Commons
Bruce E. Deagle, Austen C. Thomas, Julie C. McInnes

и другие.

Molecular Ecology, Год журнала: 2018, Номер 28(2), С. 391 - 406

Опубликована: Июнь 2, 2018

Abstract Advances in DNA sequencing technology have revolutionized the field of molecular analysis trophic interactions, and it is now possible to recover counts food sequences from a wide range dietary samples. But what do these mean? To obtain an accurate estimate consumer's diet should we work strictly with data sets summarizing frequency occurrence different taxa, or use relative number sequences? Both approaches are applied semi‐quantitative summaries, but often promoted as more conservative reliable option due taxa‐specific biases recovery sequences. We explore representative metabarcoding point out that summaries based on overestimate importance consumed small quantities (potentially including low‐level contaminants) sensitive count threshold used define occurrence. Our simulations indicate using read abundance ( RRA ) information provides view population‐level even moderate incorporated; however, impacting common taxa. when mean taxa samples small. The ideas presented here highlight need consider all sources bias justify methods interpret studies. encourage researchers continue addressing methodological challenges acknowledge unanswered questions help spur future investigations this rapidly developing area research.

Язык: Английский

Процитировано

584
Tumor-resident intracellular microbiota promotes metastatic colonization in breast cancer DOI Creative Commons
Aikun Fu,

Bingqing Yao,

Tingting Dong

и другие.

Cell, Год журнала: 2022, Номер 185(8), С. 1356 - 1372.e26

Опубликована: Апрель 1, 2022

Язык: Английский

Процитировано

580
Bacteriophages of the Human Gut: The “Known Unknown” of the Microbiome DOI Creative Commons
Andrey N. Shkoporov, Colin Hill

Cell Host & Microbe, Год журнала: 2019, Номер 25(2), С. 195 - 209

Опубликована: Фев. 1, 2019

Язык: Английский

Процитировано

578
The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific DOI Creative Commons
Andrey N. Shkoporov, Adam G. Clooney, Thomas Sutton

и другие.

Cell Host & Microbe, Год журнала: 2019, Номер 26(4), С. 527 - 541.e5

Опубликована: Окт. 1, 2019

Язык: Английский

Процитировано

570
Establishing microbial composition measurement standards with reference frames DOI Creative Commons
James T. Morton, Clarisse Marotz, Alex Washburne

и другие.

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Июнь 20, 2019

Abstract Differential abundance analysis is controversial throughout microbiome research. Gold standard approaches require laborious measurements of total microbial load, or absolute number microorganisms, to accurately determine taxonomic shifts. Therefore, most studies rely on relative data. Here, we demonstrate common pitfalls in comparing across samples and identify two solutions that reveal changes without the need estimate load. We define notion “reference frames”, which provide deep intuition about compositional nature In an oral time series experiment, reference frames alleviate false positives produce consistent results both raw cell-count normalized Furthermore, consistent, differentially abundant microbes previously undetected independent published datasets from subjects with atopic dermatitis. These methods allow reassessment data reproducible sequencing output for new assays.

Язык: Английский

Процитировано

548