Open challenges for microbial network construction and analysis

The ISME Journal, Journal Year: 2021, Volume and Issue: 15(11), P. 3111 - 3118

Published: June 9, 2021

Microbial network construction is a popular explorative data analysis technique in microbiome research. Although large number of microbial tools has been developed to date, there are several issues concerning the and interpretation networks that have received less attention. The purpose this perspective draw attention these underexplored challenges analysis.

Language: Английский

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Co-evolution and Co-speciation of Host-Gut Bacteria Systems

Cell Host & Microbe, Journal Year: 2020, Volume and Issue: 28(1), P. 12 - 22

Published: July 1, 2020

Mammalian gut microbiomes profoundly influence host fitness, but the processes that drive evolution of host-microbiome systems are poorly understood. Recent studies suggest mammals and their individual symbionts can have parallel evolutionary histories, as represented by congruent phylogenies. These "co-phylogenetic" patterns signatures ancient co-speciation events illustrate cohesiveness mammalian host-gut microbiome entity over times. Theory predicts between could result from co-evolution. However, there is only limited evidence such Here, we propose a model explains cophylogenetic without relying on Specifically, bacteria likely to diverge in recapitulating phylogeny when hosts undergo allopatric speciation, limiting inter-host bacterial dispersal genomic recombination. We provide empirically grounded series observational experimental approaches test its validity.

Language: Английский

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Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria

PLoS Biology, Journal Year: 2018, Volume and Issue: 16(7), P. e2005710 - e2005710

Published: July 5, 2018

Animals live together with diverse bacteria that can impact their biology. In Drosophila melanogaster, gut-associated bacterial communities are relatively simple in composition but also have a strong on host development and physiology. It is generally assumed gut D. melanogaster transient constant ingestion food required to maintain presence the gut. Here, we identify species from wild-caught stably associate independently of continuous inoculation. Moreover, show specific Acetobacter wild isolates proliferate We further demonstrate interaction between isolated thailandicus mutually beneficial stability association key this mutualism. The stable population allows spreading into environment, which advantageous bacterium itself. dissemination turn because next generation flies develops particularly bacterium. A. leads faster higher fertility emerging adults when compared other flies. Furthermore, sufficient axenic or freshly collected figs, respectively. This isolate colonizes several genotypes not closely related simulans, indicating specific. work establishes new conceptual model understand melanogaster–gut microbiota interactions an ecological context; be mutualistic through microbial farming, common strategy insects. these results develop use as study proliferation colonization.

Language: Английский

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Successive passaging of a plant-associated microbiome reveals robust habitat and host genotype-dependent selection

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 117(2), P. 1148 - 1159

Published: Dec. 5, 2019

There is increasing interest in the plant microbiome as it relates to both health and agricultural sustainability. One key unanswered question whether we can select for a that robust after colonization of target hosts. We used successive passaging experiment address this by selecting upon tomato phyllosphere microbiome. Beginning with diverse microbial community generated from field-grown plants, inoculated replicate plants across 5 genotypes 4 45-d passages, sequencing at each passage. observed consistent shifts bacterial (16S amplicon sequencing) fungal (internal transcribed spacer region communities lines over time, well general loss diversity course experiment, suggesting much naturally likely transient or poorly adapted within experimental setting. found host genotype environment shape composition, but relative importance declines through time. Furthermore, using coalescence end was invasion starting community. These results highlight stable particular indeed possible, emphasizing great potential approach agriculture beyond. In light response selection absence reciprocal evolution (coevolution) described here, future studies should how such adaptation influences health.

Language: Английский

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Spatial metabolomics of in situ host–microbe interactions at the micrometre scale

Nature Microbiology, Journal Year: 2020, Volume and Issue: 5(3), P. 498 - 510

Published: Feb. 3, 2020

Language: Английский

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High-order interactions distort the functional landscape of microbial consortia

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(12), P. e3000550 - e3000550

Published: Dec. 12, 2019

Understanding the link between community composition and function is a major challenge in microbial population biology, with implications for management of natural microbiomes design synthetic consortia. Specifically, it poorly understood whether functions can be quantitatively predicted from traits species monoculture. Inspired by study complex genetic interactions, we have examined how amylolytic rate combinatorial assemblages six starch-degrading soil bacteria depend on separate functional contributions each their interactions. Filtering our results through theory biochemical kinetics, show that this simple additive absence interactions among members. For about half combinatorially assembled consortia, dominated pairwise higher-order other half, despite presence strong competitive We explain mechanistic basis these findings propose quantitative framework allows us to effect behavioral dynamics Our suggest robustness consortium critically affects ability predict bottom-up engineer ecosystem communities.

Language: Английский

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Microbiome diversity protects against pathogens by nutrient blocking

Science, Journal Year: 2023, Volume and Issue: 382(6676)

Published: Dec. 14, 2023

The human gut microbiome plays an important role in resisting colonization of the host by pathogens, but we lack ability to predict which communities will be protective. We studied how bacteria influence two major bacterial both vitro and gnotobiotic mice. Whereas single species alone had negligible effects, resistance greatly increased with community diversity. Moreover, this community-level rested critically upon certain being present. explained these ecological patterns through collective resistant consume nutrients that overlap those used pathogen. Furthermore, applied our findings successfully resist a novel target strain. Our work provides reason why diversity is beneficial suggests route for rational design pathogen-resistant communities.

Language: Английский

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Transkingdom interactions between Lactobacilli and hepatic mitochondria attenuate western diet-induced diabetes

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Jan. 4, 2021

Abstract Western diet (WD) is one of the major culprits metabolic disease including type 2 diabetes (T2D) with gut microbiota playing an important role in modulating effects diet. Herein, we use a data-driven approach (Transkingdom Network analysis) to model host-microbiome interactions under WD infer which members contribute altered host metabolism. Interrogation this network pointed taxa potential beneficial or harmful on host’s We then validate functional predicted bacteria regulating metabolism and show that they act via different pathways. Our gene expression electron microscopy studies two species from Lactobacillus genus upon mitochondria liver leading improvement lipid Metabolomics analyses revealed reduced glutathione may mediate these effects. study identifies probiotic strains for T2D provides insights into mechanisms their action.

Language: Английский

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The microbiome and mosquito vectorial capacity: rich potential for discovery and translation

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: May 18, 2021

Microbiome research has gained considerable interest due to the emerging evidence of its impact on human and animal health. As in other animals, gut-associated microbiota mosquitoes affect host fitness phenotypes. It is now well established that microbes can alter pathogen transmission mosquitoes, either positively or negatively, avenues are being explored exploit for vector control. However, less attention been paid how phenotypes vectorial capacity. Several mosquito components, such as density, biting rate, survival, competence, extrinsic incubation period all influence transmission. Recent studies also indicate each these therefore ultimately modulate Promisingly, this expands options available control by targeting parameters there still many knowledge gaps regarding mosquito-microbe interactions need be addressed order them efficiently. Here, we review current impacts microbiome aspects capacity, highlight likely opportunities novel strategies areas where further required. Video abstract.

Language: Английский

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Mechanisms underlying gut microbiota–host interactions in insects

Journal of Experimental Biology, Journal Year: 2021, Volume and Issue: 224(2)

Published: Jan. 15, 2021

ABSTRACT Insects are the most diverse group of animals and colonize almost all environments on our planet. This diversity is reflected in structure function microbial communities inhabiting insect digestive system. As mammals, gut microbiota insects can have important symbiotic functions, complementing host nutrition, facilitating dietary breakdown or providing protection against pathogens. There an increasing number models that experimentally tractable, mechanistic studies microbiota–host interactions. In this Review, we will summarize recent findings advanced understanding molecular mechanisms underlying symbiosis between their microbiota. We open article with a general introduction to then turn towards discussion particular processes governing colonization environment as well beneficial roles mediated by The Review highlights that, although active field research implications for fundamental applied science, still early stage mechanisms. However, expanding capability culture microbiomes manipulate microbe–host interactions promises new insights from symbioses.

Language: Английский

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