Evaluating the core microbiota in complex communities: A systematic investigation

Environmental Microbiology, Journal Year: 2017, Volume and Issue: 19(4), P. 1450 - 1462

Published: Jan. 12, 2017

Summary The study of complex microbial communities poses unique conceptual and analytical challenges, with species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a ‘core’ microbiota approach, focusing only on stable permanent members community, is becoming increasingly popular. Given various ways defining core microbiota, it prudent examine whether definition impacts upon results obtained. Here we used marine sponge microbiotas undertook systematic evaluation degree which different factors define influenced conclusions. Significant differences alpha‐ beta‐diversity were detected using some but not all definitions. However, findings related host specificity environmental quality largely insensitive major changes definition. Furthermore, none applied definitions altered our perception ecological networks summarising interactions among bacteria within sponges. These suggest that, while care should still be taken interpretation, approach surprisingly robust, at least for comparing closely samples.

Language: Английский

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Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean

Frontiers in Marine Science, Journal Year: 2017, Volume and Issue: 4

Published: July 18, 2017

All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal-microbial relationships have historically been explored in single host-symbiont systems. However, new explorations into diversity of microorganisms associating diverse marine animal hosts is moving field studies that address interactions between host a more microbiome. The potential for microbiomes to influence health, physiology, behavior ecology could alter current understandings how adapt change, especially growing climate-related anthropogenic-induced changes already impacting ocean environment. This review explores nature animal-microbiome interactions, possible factors may shift from symbiotic dissociated states. I present brief microbiome research opportunities, using examples select span phyla within Animalia, systems are less developed symbiosis research, two represented my own program. Lastly, consider challenges emerging solutions these other study detailed understanding host-microbiome changing ocean.

Language: Английский

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Microbial contributions to the persistence of coral reefs

The ISME Journal, Journal Year: 2017, Volume and Issue: 11(10), P. 2167 - 2174

Published: May 16, 2017

On contemplating the adaptive capacity of reef organisms to a rapidly changing environment, microbiome offers significant and greatly unrecognised potential. Microbial symbionts contribute physiology, development, immunity behaviour their hosts, can respond very environmental conditions, providing powerful mechanism for acclimatisation also possibly rapid evolution coral holobionts. Environmentally acquired fluctuations in have functional consequences holobiont phenotype upon which selection act. induced changes microbial abundance may be analogous host gene duplication, symbiont switching / shuffling as result change either remove or introduce raw genetic material into holobiont; horizontal transfer facilitate within strains. Vertical transmission is key feature many holobionts this would enable environmentally traits faithfully passed future generations, ultimately facilitating microbiome-mediated transgenerational (MMTA) potentially even adaptation species climate. In commentary, we highlight mechanisms MMTA species, propose modified Price equation framework assessing recommend areas research better understand how microorganisms organisms, essential if are reliably predict global ecosystems.

Language: Английский

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Predicting the HMA-LMA Status in Marine Sponges by Machine Learning

Frontiers in Microbiology, Journal Year: 2017, Volume and Issue: 8

Published: May 8, 2017

The dichotomy between high microbial abundance (HMA) and low (LMA) sponges has been observed in sponge-microbe symbiosis, although the extent of this pattern remains poorly unknown. We characterized differences microbiomes HMA (n = 19) LMA 17) (575 specimens) present Sponge Microbiome Project. were associated with richer more diverse than sponges, as indicated by comparison alpha diversity metrics. Microbial community structures differed considering Operational Taxonomic Units (OTU) abundances across taxonomic levels, from phylum to species. largest proportion microbiome variation was explained host identity. Several phyla, classes, OTUs found differentially abundant either group, which considered "HMA indicators" "LMA indicators." Machine learning algorithms (classifiers) trained predict HMA-LMA status sponges. Among nine different classifiers, higher performances achieved Random Forest class abundances. optimized parameters predicted additional 135 sponge species (1,232 without a priori knowledge. These grouped four clusters, two composed consistently 44) 74). In summary, our analyses shown distinct features communities prediction based on profiles demonstrates application machine explore patterns host-associated communities.

Language: Английский

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Host specificity of the gut microbiome

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 19(10), P. 639 - 653

Published: May 27, 2021

Language: Английский

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Core gut microbial communities are maintained by beneficial interactions and strain variability in fish

Nature Microbiology, Journal Year: 2019, Volume and Issue: 4(12), P. 2456 - 2465

Published: Sept. 23, 2019

Language: Английский

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A social niche breadth score reveals niche range strategies of generalists and specialists

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(5), P. 768 - 781

Published: April 3, 2023

Abstract Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although classical concept ecology, niche breadth has remained challenging quantify for microorganisms because it depends on an objective definition of the Here, by defining environment microorganism as community resides in, we integrated information from over 22,000 environmental sequencing samples derive quantitative measure niche, which call social breadth. At level genera, explored range strategies throughout prokaryotic tree life. We found that generalists include opportunists stochastically dominate local communities, stable but low abundance. Social have more diverse and open pan-genome than specialists, no global correlation between genome size. Instead, observed two distinct evolutionary strategies, whereby relatively small genomes habitats with diversity, large high diversity. Together, our analysis shines data-driven light microbial strategies.

Language: Английский

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The role of animal hosts in shaping gut microbiome variation

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 379(1901)

Published: March 18, 2024

Millions of years co-evolution between animals and their associated microbial communities have shaped diversified the nature relationship. Studies continue to reveal new layers complexity in host–microbe interactions, fate which depends on a variety different factors, ranging from neutral processes environmental factors local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics mathematical modelling disentangle individual contribution ecological microbiome evolution. Within this framework, host are known be among dominant drivers composition animal species. However, extent they shape assembly evolution remains unclear. In review, we summarize our understanding how drive these dynamics conserved vary across taxa. We conclude by outlining key avenues for research highlight need implementation modifications existing theory fully capture host-associated microbiomes. This article part theme issue ‘Sculpting microbiome: determine respond colonization’.

Language: Английский

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Lessons from the Environmental Antibiotic Resistome

Annual Review of Microbiology, Journal Year: 2017, Volume and Issue: 71(1), P. 309 - 329

Published: June 28, 2017

Antibiotic resistance is a global public health issue of growing proportions. All antibiotics are susceptible to resistance. The evidence now clear that the environment single largest source and reservoir Soil, aquatic, atmospheric, animal-associated, built ecosystems home microbes harbor antibiotic elements means mobilize them. diversity abundance in consistent with ancient origins variety studies support long natural history associated implications clear: Understanding evolution environment, its diversity, mechanisms essential management our existing future resources.

Language: Английский

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Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

The ISME Journal, Journal Year: 2017, Volume and Issue: 11(11), P. 2465 - 2478

Published: July 11, 2017

Marine sponges are ancient metazoans that populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read PacBio long-read sequencing followed un-targeted metagenomic binning. We identified a total 37 high-quality bins representing 11 bacterial phyla two candidate phyla. Statistical comparison symbiont genomes with selected reference revealed significant enrichment genes related defense (restriction-modification systems, toxin-antitoxin systems) as well involved in host colonization extracellular matrix utilization symbionts. A within-symbionts genome nutritional specialization at least guilds, where one appears metabolize carnitine other sulfated polysaccharides, both which abundant molecules matrix. third guild symbionts may be viewed generalists perform largely same metabolic pathways but lack such extraordinary numbers relevant genes. This study characterizes genomic an unprecedented resolution it provides greater molecular mechanisms underlying microbial-sponge symbiosis.

Language: Английский

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