Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams DOI Creative Commons
Susheel Bhanu Busi, Massimo Bourquin, Stilianos Fodelianakis

и другие.

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Апрель 20, 2022

In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that seize this in an otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning entire tree life including rich virome. Various co-existing energy acquisition pathways point niches exploitation available resources, likely fostering establishment during opportunity. The wide occurrence rhodopsins, besides chlorophyll, highlights role solar capture these while internal carbon nutrient cycling between photoautotrophs heterotrophs may help overcome constraints imposed oligotrophy habitats. Mechanisms potentially protecting bacteria against low temperatures high UV-radiation are also revealed selective pressure environment is further highlighted phylogenomic analysis differentiating important components stream from other ecosystems. Our findings reveal genomic underpinnings adaptive traits contributing success exploit opportunities which now rapidly changing owing global warming.

Язык: Английский

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data DOI

Jasmine Chong,

Peng Liu,

Guangyan Zhou

и другие.

Nature Protocols, Год журнала: 2020, Номер 15(3), С. 799 - 821

Опубликована: Янв. 15, 2020

Язык: Английский

Процитировано

1425
Tara Oceans: towards global ocean ecosystems biology DOI
Shinichi Sunagawa, Silvia G. Acinas, Peer Bork

и другие.

Nature Reviews Microbiology, Год журнала: 2020, Номер 18(8), С. 428 - 445

Опубликована: Май 12, 2020

Язык: Английский

Процитировано

373
microViz: an R package for microbiome data visualization and statistics DOI Creative Commons
David Barnett, Ilja C.W. Arts, John Penders

и другие.

The Journal of Open Source Software, Год журнала: 2021, Номер 6(63), С. 3201 - 3201

Опубликована: Июль 10, 2021

microViz is an R package for the statistical analysis and visualization of microbiota data.This extends functionality popular microbial ecosystem data packages, including phyloseq (McMurdie & Holmes, 2013), vegan (Oksanen et al., 2020) microbiome (Lahti Shetty, 2012-2019).microViz provides a selection powerful additions to toolbox researchers already familiar with microbiome, as well assisting less programming experience independently explore analyse their generate publication-ready figures.

Язык: Английский

Процитировано

252
A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors DOI Creative Commons

Anders B. Dohlman,

Jared Klug,

Marissa Mesko

и другие.

Cell, Год журнала: 2022, Номер 185(20), С. 3807 - 3822.e12

Опубликована: Сен. 1, 2022

Язык: Английский

Процитировано

248
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere DOI Creative Commons
Robyn Wright, Morgan G. I. Langille, Tony R. ‎Walker

и другие.

The ISME Journal, Год журнала: 2020, Номер 15(3), С. 789 - 806

Опубликована: Ноя. 2, 2020

Abstract It is now indisputable that plastics are ubiquitous and problematic in ecosystems globally. Many suggestions have been made about the role biofilms colonizing environment—termed “Plastisphere”—may play transportation ecological impact of these plastics. By collecting re-analyzing all raw 16S rRNA gene sequencing metadata from 2,229 samples within 35 studies, we performed first meta-analysis Plastisphere marine, freshwater, other aquatic (e.g., brackish or aquaculture) terrestrial environments. We show random forest models can be trained to differentiate between groupings environmental factors as well aspects study design, but—crucially—also when compared with control different plastic types community successional stages. Our confirms potentially biodegrading members, hydrocarbonoclastic Oceanospirillales Alteromonadales consistently more abundant than biofilm across multiple studies This indicates predilection organisms for urgent need their ability biodegrade comprehensively tested. also identified key knowledge gaps should addressed by future studies.

Язык: Английский

Процитировано

212
Best practices in metabarcoding of fungi: From experimental design to results DOI Open Access
Leho Tedersoo,

Mohammad Bahram,

Lucie Zinger

и другие.

Molecular Ecology, Год журнала: 2022, Номер 31(10), С. 2769 - 2795

Опубликована: Апрель 8, 2022

The development of high-throughput sequencing (HTS) technologies has greatly improved our capacity to identify fungi and unveil their ecological roles across a variety ecosystems. Here we provide an overview current best practices in metabarcoding analysis fungal communities, from experimental design through molecular computational analyses. By reanalysing published data sets, demonstrate that operational taxonomic units (OTUs) outperform amplified sequence variants (ASVs) recovering diversity, finding is particularly evident for long markers. Additionally, the full-length ITS region allows more accurate placement other eukaryotes compared ITS2 subregion. Finally, show specific methods compositional analyses reliable estimates shifts community structure. We conclude are especially promising integrating into full microbiome broader ecosystem functioning context, recovery novel lineages ancient organisms as well barcoding old specimens including type material.

Язык: Английский

Процитировано

194
Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens DOI Creative Commons
Jacqueline M. Leung, Andrea L. Graham, Sarah C. L. Knowles

и другие.

Frontiers in Microbiology, Год журнала: 2018, Номер 9

Опубликована: Май 14, 2018

The vertebrate gut teems with a large, diverse, and dynamic bacterial community that has pervasive effects on physiology, metabolism, immunity. Under natural conditions, these microbes share their habitat similarly of eukaryotes (helminths, protozoa, fungi), many which are well-known parasites. Both parasites the prokaryotic microbiota can dramatically alter physical immune landscape gut, creating ample opportunities for them to interact. Such interactions may critically infection outcomes affect overall host health disease. For instance, parasite change how interacts its flora, either driving or protecting against dysbiosis inflammatory Conversely, parasite's colonization success, replication, virulence, shifting it along parasitism-mutualism spectrum. mechanisms consequences just starting be elucidated in an emergent transdisciplinary area at boundary microbiology parasitology. However, heterogeneity experimental designs, species, largely phenomenological taxonomic approach synthesizing literature have meant common themes across studies remain elusive. Here, we use ecological perspective review between eukaryotic gut. Using knowledge about biology ecology, discuss by they interact microbes, such health, understanding parasite-microbiota lead novel approaches disease control.

Язык: Английский

Процитировано

180
Rotavirus vaccine response correlates with the infant gut microbiota composition in Pakistan DOI Open Access
Vanessa Harris, Asad Ali, Susana Fuentes

и другие.

Gut Microbes, Год журнала: 2017, Номер 9(2), С. 93 - 101

Опубликована: Сен. 11, 2017

Rotavirus (RV) is the leading cause of diarrhea-related death in children worldwide and ninety-five percent rotavirus deaths occur Africa Asia. vaccines (RVV) can dramatically reduce RV deaths, but have low efficacy low-income settings where they are most needed. The intestinal microbiome may contribute to this decreased RVV efficacy. This pilot study hypothesizes that infants' microbiota composition correlates with immune responses responders different gut as compared non-responders. We conducted a nested, matched case-control comparing pre-vaccination between 10 6-week old Pakistani RVV-responders, non-responders, healthy Dutch infants. response was defined an Immunoglobulin A ≥20 IU/mL following Rotarix™(RV1) vaccination infant IgA<20. Infants were 1:1 ratio using ranked variables: RV1 dosing schedule (6/10/14; 6/10; or 10/14 weeks), season, delivery mode, place, breastfeeding practices, age gender. Fecal analysis performed highly reproducible phylogenetic microarray. correlated higher relative abundance bacteria belonging Clostridium cluster XI Proteobacteria, including related Serratia Escherichia coli. Remarkably, these Proteobacteria also significantly infants when RV1-non-responders Pakistan. small carefully showed correlate seroconversion Pakistan infants, identifying signatures shared

Язык: Английский

Процитировано

177
The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants DOI Creative Commons

Anders B. Dohlman,

Diana Arguijo Mendoza,

Shengli Ding

и другие.

Cell Host & Microbe, Год журнала: 2021, Номер 29(2), С. 281 - 298.e5

Опубликована: Янв. 10, 2021

Язык: Английский

Процитировано

172
A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss) DOI Creative Commons
Jacob Agerbo Rasmussen,

Kasper Rømer Villumsen,

Madeleine Ernst

и другие.

Microbiome, Год журнала: 2022, Номер 10(1)

Опубликована: Янв. 30, 2022

Abstract Background Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health sustainability. Here, we investigate functional effects bacteria-based pro- synbiotic feed additives on functions in relation growth performance commercially important rainbow trout ( Oncorhynchus mykiss ). We combine complementary insights from multiple omics datasets content samples, including 16S bacterial profiling, whole metagenomes, untargeted metabolomics, metagenome-assembled genomes (MAGs) their molecular interactions with host metabolism. Results Our findings reveal that (I) changed microbiome reared had a significantly reduced relative abundance salmonid related Candidatus Mycoplasma salmoninae both mid distal content, (II) genome resolved metagenomics revealed alterations microbial arginine biosynthesis terpenoid backbone synthesis pathways were directly associated presence salmoninae, (III) differences composition intestinal microbiota among types significant changes metabolomic landscape, lipids lipid-like metabolites, amino acids, bile steroid-related metabolites. Conclusion results demonstrate how use multi-omics complex host-microbiome enable us evaluate potential probiotics compared studies only measure overall or characterise environments.

Язык: Английский

Процитировано

87