Universal gut microbial relationships in the gut microbiome of wild baboons DOI Creative Commons
Kimberly Roche, Johannes R. Björk, Mauna Dasari

et al.

eLife, Journal Year: 2023, Volume and Issue: 12

Published: May 9, 2023

Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing overall direction and strength of these is essential learn how ecology scales up affect microbiome assembly, dynamics, host health. However, whether bacterial are generalizable across hosts or personalized individual debated. Here, we apply a robust, multinomial logistic-normal modeling framework extensive time series data (5534 samples from 56 baboon over 13 years) infer thousands correlations in abundance baboons test degree which 'universal'. We also compare patterns two human sets. find that, most weak, negative, universal hosts, such shared correlation dominate host-specific by almost twofold. Further, taxon pairs had inconsistent signs (either positive negative) different always weak within From perspective, with similar taxonomic compositions tended be genetic relatives. Compared humans, universality was infants, stronger than one set adults. Bacterial families showed infants were often baboons. Together, our work contributes new tools for analyzing associations implications personalization, community stability, designing interventions improve health.Communities living guts humans other animals perform as digesting food, degrading toxins, fighting viruses cause disease. These emerge so-called ‘ecological’ species bacteria. One species, example, may break down molecule food into another compound is, turn, digested small can absorb use. The involved process become more less common together host. In situations, some have opposing roles each other, meaning if becomes abundant it reduce level other. not known consistent (i.e., universal) unique (personalized). words, pair increase decrease host, do they same hosts? Microbes swap genes gain traits; harbors distinctive microbes, possible microbial change depending on present specific environment. To investigate, Roche et al. studied feces collected 13-year period. came long-term research project Amboseli, Kenya has been studying population wild continuously since 1971. measured hundreds understand pairs. This revealed connections largely rather baboon. Furthermore, strongest negative Microbial strong effects microbiome’s composition might therefore especially universal. Further analyses measuring babies found Hence, fill ecological primates, perhaps mammals. findings suggest leverage develop therapies diseases associated bacteria, inflammatory bowel disease Clostridium difficile infection.

Language: Английский

Biophysical processes supporting the diversity of microbial life in soil DOI Creative Commons
Robin Tecon, Dani Or

FEMS Microbiology Reviews, Journal Year: 2017, Volume and Issue: 41(5), P. 599 - 623

Published: July 10, 2017

Soil, the living terrestrial skin of Earth, plays a central role in supporting life and is home to an unimaginable diversity microorganisms. This review explores key drivers for microbial soils under different climates land-use practices at scales ranging from soil pores landscapes. We delineate special features as habitat (focusing on bacteria) consequences communities. covers recent modeling advances that link physical processes with (termed biophysical processes). Readers are introduced concepts governing water organization associated transport properties dispersion ranges often determined by spatial highly dynamic aqueous phase. The narrow hydrological windows wetting phase connectedness crucial resource distribution longer range Feedbacks between activity their immediate environment responsible emergence stabilization structure-the scaffolding ecological functioning. synthesize insights historical contemporary studies provide outlook challenges opportunities developing quantitative framework predict component

Language: Английский

Citations

438
Toxicity drives facilitation between 4 bacterial species DOI Creative Commons

Philippe Piccardi,

Björn Vessman,

Sara Mitri

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(32), P. 15979 - 15984

Published: July 3, 2019

Competition between microbes is extremely common, with many investing in mechanisms to harm other strains and species. Yet positive interactions species have also been documented. What makes help or each currently unclear. Here, we studied the 4 bacterial capable of degrading metal working fluids (MWF), an industrial coolant lubricant, which contains growth substrates as well toxic biocides. We were surprised find only neutral Using mathematical modeling further experiments, show that this community likely due toxicity MWF, whereby species' detoxification benefited others by facilitating their survival, such they could grow degrade MWF better when together. The addition nutrients, reduction toxicity, more instead resulted competitive behavior. Our work provides support stress gradient hypothesis showing how harsh, environments can strongly favor facilitation microbial mask underlying interactions.

Language: Английский

Citations

264
Quorum sensing for population-level control of bacteria and potential therapeutic applications DOI
Shengbo Wu, Jiaheng Liu, Chunjiang Liu

et al.

Cellular and Molecular Life Sciences, Journal Year: 2019, Volume and Issue: 77(7), P. 1319 - 1343

Published: Oct. 14, 2019

Language: Английский

Citations

159
Sharing vitamins: Cobamides unveil microbial interactions DOI
Olga M. Sokolovskaya, Amanda N. Shelton, Michiko E. Taga

et al.

Science, Journal Year: 2020, Volume and Issue: 369(6499)

Published: July 2, 2020

Nutritional interdependencies Bacteria and archaea show a wide range of nutritional specialism. Not every organism can synthesize essential components may need to trade for them. Taking as an example diverse interesting family enzyme cofactors—the cobalt-containing cobamides, which include vitamin B 12 —Sokolovskaya et al. reviewed the among microorganisms this suite nutrients. Cobamides are required many processes, from catabolism carbon sources nucleotide biosynthesis, needed by majority microbes, those in gut oceans. Availability cobamides is patchy habitat specific, nonspecific scavenging not be adequate obtain specific cobamide structure organism. Therefore, variety mutualisms have evolved deliver import structural variants between organisms or consortia eukaryotes prokaryotes equal subtle distinct mechanisms. Science , issue p. 48

Language: Английский

Citations

159
Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities DOI Creative Commons
Ruiwen Hu, Hai-Ming Zhao, Xihui Xu

et al.

Environment International, Journal Year: 2021, Volume and Issue: 154, P. 106560 - 106560

Published: April 16, 2021

The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats human health, it is urgent develop efficient strategies eliminate them from Bacteria-driven PAE biodegradation been considered as an inexpensive yet effective strategy restore the contaminated Despite great advances in bacterial culturing and sequencing, inherent complexity indigenous microbial community hinders us mechanistically understand situ efficiently harness degrading power bacteria. synthetic ecology provides a simple controllable model system address this problem. In review, we focus on current progress mediated by isolates communities, discuss prospective PAE-degrading communities research. It anticipated that theories approaches will revolutionize study bacteria-driven provide novel insights for developing bioremediation solutions.

Language: Английский

Citations

126
Soil microbiome engineering for sustainability in a changing environment DOI
Janet Jansson, Ryan McClure, Robert G. Egbert

et al.

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 41(12), P. 1716 - 1728

Published: Oct. 30, 2023

Language: Английский

Citations

106
Mechanisms and implications of bacterial–fungal competition for soil resources DOI Creative Commons
Chaoqun Wang, Yakov Kuzyakov

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Abstract Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, functions in soil, as well regulate carbon (C) nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources main factor determining adaptation niche differentiation these two big groups soil. This because C energy limitations growth are a rule rather than an exception. Here, we review demands of fungi—the major kingdoms soil—the mechanisms their other resources, leading differentiation, global change impacts on this competition. The normalized utilization preference showed 1.4–5 times more efficient uptake simple organic compounds substrates, whereas 1.1–4.1 effective utilizing compounds. Accordingly, strongly outcompete while take advantage Bacteria also compete with products released during degradation substrates. Based specifics, differentiated spatial, temporal, chemical niches will increase under five changes including elevated CO2, N deposition, soil acidification, warming, drought. Elevated warming bacterial dominance, acidification drought fungal competitiveness.

Language: Английский

Citations

94
Production of chemicals using dynamic control of metabolic fluxes DOI
Peng Xu

Current Opinion in Biotechnology, Journal Year: 2017, Volume and Issue: 53, P. 12 - 19

Published: Nov. 14, 2017

Language: Английский

Citations

116
Understanding the evolution of interspecies interactions in microbial communities DOI Open Access
Florien A. Gorter, Michael Manhart, Martin Ackermann

et al.

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2020, Volume and Issue: 375(1798), P. 20190256 - 20190256

Published: March 23, 2020

Microbial communities are complex multi-species assemblages that characterized by a multitude of interspecies interactions, which can range from mutualism to competition. The overall sign and strength interactions have important consequences for emergent community-level properties such as productivity stability. It is not well understood how change over evolutionary timescales. Here, we review the empirical evidence evolution an driver microbial community dynamics on timescales traditionally been regarded purely ecological. Next, briefly discuss different modelling approaches study communities, emphasizing similarities differences between ecological perspectives. We then propose simple conceptual model in communities. Specifically, understand it distinguish direct indirect fitness effects mutation. predict well-mixed environments, traits will be selected exclusively their effects, while spatially structured may also effects. Selection indirectly beneficial should result increase interaction time, selection directly systematic effect. tested our intuitions using quantitative found support hypotheses. next step test these hypotheses experimentally provide input more refined version turn, thus closing scientific cycle models experiments. This article part theme issue 'Conceptual challenges ecology'.

Language: Английский

Citations

101
Stress-induced metabolic exchanges between complementary bacterial types underly a dynamic mechanism of inter-species stress resistance DOI Creative Commons
Kapil Amarnath, Avaneesh V. Narla, Sammy Pontrelli

et al.

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 31, 2023

Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, the forces driving extensive needed to support coexistence free-living are poorly understood. Here we characterize bacterial physiology under self-acidification and establish that excretion key metabolites following growth arrest provides a collaborative, inter-species mechanism stress resistance. This collaboration occurs not only between species isolated from same community, but also unrelated with complementary (glycolytic vs. gluconeogenic) modes metabolism. Cultures such communities progress through distinct phases growth-dilution cycles, comprising exponential acidification-triggered arrest, collaborative deacidification, recovery, each phase involving different combinations physiological states individual species. Our findings challenge steady-state view ecosystems commonly portrayed models, offering an alternative dynamical based advantages phases.

Language: Английский

Citations

33