Spatial structure in the “Plastisphere”: Molecular resources for imaging microscopic communities on plastic marine debris DOI
Cathleen Schlundt, Jessica L. Mark Welch, Anna M. Knochel

et al.

Molecular Ecology Resources, Journal Year: 2019, Volume and Issue: 20(3), P. 620 - 634

Published: Nov. 29, 2019

Abstract Plastic marine debris (PMD) affects spatial scales of life from microbes to whales. However, understanding interactions between plastic and in the “Plastisphere”—the thin layer on surface PMD—has been technology‐limited. Research into microbe–microbe microbe–substrate requires knowledge community phylogenetic composition but also tools visualize distributions intact microbial biofilm communities. We developed a CLASI‐FISH (combinatorial labelling spectral imaging – fluorescence situ hybridization) method using confocal microscopy study Plastisphere created probe set consisting three existing probes (targeting all Bacteria, Alpha ‐, Gammaproteobacteria ) four newly designed Bacteroidetes , Vibrionaceae Rhodobacteraceae Alteromonadaceae labelled with total seven fluorophores validated this pure cultures. Our nested strategy increases confidence taxonomic identification because targets are confirmed two or more probes, reducing false positives. simultaneously identified visualized these taxa their distribution within biofilms polyethylene samples colonization time series experiments coastal environments different biogeographical regions. Comparing relative abundance 16S rRNA gene amplicon sequencing data cell‐count retrieved microscope images same showed good agreement bacterial composition. Microbial communities were heterogeneous, direct relationships bacteria, cyanobacteria eukaryotes such as diatoms micro‐metazoa. research provides valuable resource investigate development, succession associations specific microscopic at micrometre scales.

Language: Английский

The Role of the Gastrointestinal Mucus System in Intestinal Homeostasis: Implications for Neurological Disorders DOI Creative Commons
Madushani Herath, Suzanne Hosie, Joel C. Bornstein

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2020, Volume and Issue: 10

Published: May 28, 2020

Mucus is integral to gut health and its properties may be affected in neurological disease. The mucus lining of the gastrointestinal (GI) tract plays a prominent role physically preventing microbial content reaching intestinal epithelium. Multiple factors influence volume, viscosity, porosity GI tract, including proliferation mucus-secreting goblet cells from stem located at base crypts. Via number mechanisms, abnormalities neuronal networks occurring disorders alter structure function patients. has own intrinsic network, enteric nervous system, which extends length innervates mucosal commensal microbiota mood behavior via neural non-neural pathways within gut-brain axis. Both dysbiosis dysfunction are commonly reported several such as Parkinson's Alzheimer's disease well patients with neurodevelopmental autism. Since some microbes use energy source, changes could alter, even exacerbate, dysbiosis-related symptoms disorders. This review summarizes existing knowledge highlights areas addressed future research better understand how homeostasis impacted

Language: Английский

Citations

172
Highly multiplexed spatial mapping of microbial communities DOI
Hao Shi, Qiaojuan Shi, Benjamin Grodner

et al.

Nature, Journal Year: 2020, Volume and Issue: 588(7839), P. 676 - 681

Published: Dec. 2, 2020

Language: Английский

Citations

168
Spatial Ecology of the Human Tongue Dorsum Microbiome DOI Creative Commons
Steven A. Wilbert, Jessica L. Mark Welch, Gary G. Borisy

et al.

Cell Reports, Journal Year: 2020, Volume and Issue: 30(12), P. 4003 - 4015.e3

Published: March 1, 2020

A fundamental question in microbial ecology is how microbes are spatially organized with respect to each other and their host. test bed for examining this the tongue dorsum, which harbors a complex important community. Here, we use multiplexed fluorescence spectral imaging investigate organization of microbiome at micron hundred-micron scales. We design oligonucleotide probes taxa both abundant prevalent, as determined by sequence analysis. Imaging reveals highly structured spatial consortia, ranging linear dimension from tens hundreds microns. The consortia appear develop core epithelial cells, clustering domains suggestive clonal expansion. Quantitative proximity analysis provides basis model dorsum dynamics. Our work illustrates high-resolution micron-scale insights into physiological functions microbiome-host interactions.

Language: Английский

Citations

152
HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases DOI Creative Commons
Ivan Vujkovic-Cvijin,

Ornella Sortino,

Eveline Verheij

et al.

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: May 15, 2020

Abstract Loss of gut mucosal integrity and an aberrant microbiota are proposed mechanisms contributing to chronic inflammation increased morbidity mortality during antiretroviral-treated HIV disease. Sexual practice has recently been uncovered as a major source variation, potentially confounding prior observations alterations among persons with (PWH). To overcome this other factors, we examine well-powered subset AGEhIV Cohort participants comprising PWH seronegative controls matched for age, body-mass index, sex, sexual practice. We report significant differences in regardless sex including Gammaproteobacteria enrichment, Lachnospiraceae Ruminococcaceae depletion, decreased alpha diversity. Men who have men (MSM) exhibit distinct signature characterized by Prevotella enrichment diversity, which is linked receptive anal intercourse both males females. Finally, the HIV-associated correlates inflammatory markers suPAR, nadir CD4 count, prevalence age-associated noncommunicable comorbidities.

Language: Английский

Citations

144
Microbiota in Tumors: From Understanding to Application DOI
Yifan Xie, Feng Xie, Xiaoxue Zhou

et al.

Advanced Science, Journal Year: 2022, Volume and Issue: 9(21)

Published: May 23, 2022

Microbes with complex functions have been found to be a potential component in tumor microenvironments. Due their low biomass and other obstacles, intratumor microbiota is poorly understood. Mucosal sites normal adjacent tissues are important sources of microbiota, while hematogenous spread also leads the invasion microbes. Intratumor affects progression tumors through several mechanisms, such as DNA damage, activation oncogenic pathways, induction immunosuppression, metabolization drugs. Notably, different types tumors, composition abundance highly heterogeneous may play roles tumors. Because concern this field, techniques omics immunological methods used study microbiota. Here, recent progress field reviewed, including related heterogeneity. Techniques that can discussed. Moreover, research summarized into development strategies antitumor treatment prospects for possible future field.

Language: Английский

Citations

119
Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota DOI Creative Commons
Andrés Aranda-Díaz, Katharine M. Ng,

Tani Thomsen

et al.

Cell Host & Microbe, Journal Year: 2022, Volume and Issue: 30(2), P. 260 - 272.e5

Published: Jan. 19, 2022

Language: Английский

Citations

90
Spatial metatranscriptomics resolves host–bacteria–fungi interactomes DOI Creative Commons
Sami Saarenpää, Or Shalev, Haim Ashkenazy

et al.

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(9), P. 1384 - 1393

Published: Nov. 20, 2023

The interactions of microorganisms among themselves and with their multicellular host take place at the microscale, forming complex networks spatial patterns. Existing technology does not allow simultaneous investigation between a multitude its colonizing microorganisms, which limits our understanding host-microorganism within plant or animal tissue. Here we present metatranscriptomics (SmT), sequencing-based approach that leverages 16S/18S/ITS/poly-d(T) multimodal arrays for transcriptome- microbiome-wide characterization tissues 55-µm resolution. We showcase SmT in outdoor-grown Arabidopsis thaliana leaves as model system, find tissue-scale bacterial fungal hotspots. By network analysis, study inter- intrakingdom well response to microbial provides an answering fundamental questions on host-microbiome interplay.

Language: Английский

Citations

50
Mechanistic Insights Into the Cross-Feeding of Ruminococcus gnavus and Ruminococcus bromii on Host and Dietary Carbohydrates DOI Creative Commons

Emmanuelle H. Crost,

Gwénaëlle Le Gall,

Jenny A. Laverde-Gomez

et al.

Frontiers in Microbiology, Journal Year: 2018, Volume and Issue: 9

Published: Nov. 5, 2018

Dietary and host glycans shape the composition of human gut microbiota with keystone carbohydrate-degrading species playing a critical role in maintaining structure function microbial communities. Here we focused on two major symbionts, mucin-degrader Ruminococcus gnavus ATCC 29149, bromii L2-63, for degradation resistant starch colon. Using anaerobic individual co-cultures R. grown mucin or as sole carbon source, showed that by supported growth whereas did not benefit from gnavus. Further analyzed (quantitative PCR), metabolite production (1H-NMR analysis), bacterial transcriptional response (RNA-seq) cultured (RS) soluble (SS) presence absence In co-culture fermentations starch, 1H-NMR analysis benefits transient glucose malto-oligosaccharides released upon degradation, producing acetate, formate, lactate main fermentation end-products. Differential expression (DESeq 2) (SS RS) induced changes genes encoding several maltose transporters enzymes involved its metabolism such phosphorylase, line ability to utilize products. RS co-culture. significant increase induction tryptophan biosynthesis decrease VitB12-dependant methionine compared mono-culture, suggesting Trp VitB12 availability become limited Together this study direct competition between RS, vivo, population inhabiting mucus niche may be modulated supply non-digestible carbohydrates reaching colon RS.

Language: Английский

Citations

142
Microbiota-gut brain axis involvement in neuropsychiatric disorders DOI
Luigi Francesco Iannone, Alberto Preda, Hervé M. Blottière

et al.

Expert Review of Neurotherapeutics, Journal Year: 2019, Volume and Issue: 19(10), P. 1037 - 1050

Published: July 1, 2019

Introduction: The microbiota-gut brain (MGB) axis is the bidirectional communication between intestinal microbiota and brain. An increasing body of preclinical clinical evidence has revealed that gut microbial ecosystem can affect neuropsychiatric health. However, there still a need further studies to elucidate complex gene-environment interactions role MGB in diseases, with aim identifying biomarkers new therapeutic targets, allow early diagnosis improving treatments. Areas covered: To review disorders, prediction prevention disease through exploitation, integration, combination data from existing microbiome/microbiota projects appropriate other International '-Omics' studies. authors also evaluated technological advances investigate modulate, nutritional interventions, microbiota. Expert opinion: have documented an association alterations composition and/or function, whereas support for impacting behaviors which are relevance psychiatry central nervous system (CNS) disorders. Targeting could be additional approach treating CNS disorders all conditions involved.

Language: Английский

Citations

142
Spatial metagenomic characterization of microbial biogeography in the gut DOI
Ravi U. Sheth, Mingqiang Li, Weiqian Jiang

et al.

Nature Biotechnology, Journal Year: 2019, Volume and Issue: 37(8), P. 877 - 883

Published: July 22, 2019

Language: Английский

Citations

128