Microbiome rescue: directing resilience of environmental microbial communities

Shade, Ashley

doi:10.1016/j.mib.2022.102263

Cited by 23 publications

(14 citation statements)

References 66 publications

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“…This is in agreement with previous findings in a study involving fecal samples from healthy Belgian women collected over 6 weeks, where within-individual Bray-Curtis distances fell between 0.25 and 0.5 1 . We detected a negative correlation between functional redundancy and the scale of perturbation, consistent with previous studies suggesting that high redundancy contributes to stable functioning in a microbiome community under external perturbation 37 . We found a positive correlation between functional redundancy and the extent of perturbation upon antibiotics exposure and established the fragility index as a proxy to comprehensively describe resilience in a microbiome context.…”

Section: 𝐹𝑟𝑎𝑔𝑖𝑙𝑖𝑡𝑦 𝑖𝑛𝑑𝑒𝑥 = 𝐸𝑠𝑡𝑖𝑚𝑎𝑡𝑒𝑑 𝑟𝑒𝑐𝑜𝑣𝑒𝑟𝑒𝑑 𝑡𝑖𝑚𝑒 × 𝐷𝑖𝑠𝑠𝑖𝑚𝑖𝑙𝑎𝑟𝑖𝑡𝑦 𝑢...supporting

confidence: 91%

Baseline microbiome composition impacts resilience to and recovery following antibiotics

Chen,

Löber,

Bartolomaeus

et al. 2024

Preprint

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The gut microbiome of healthy individuals naturally undergoes temporal changes linked to the dynamics of its community components. These dynamics are only observable in longitudinal studies; they are particularly relevant to understanding ecosystem responses to external environment disturbances. External exposures, such as antibiotic treatment, significantly reshape the gut microbiome, impacting both pathogen and commensal microbes. The gut microbiome plays pivotal roles in digestion, nutrient absorption, and mental health, influencing immune systems, obesity, and various diseases. Consequently, beyond the short-term effects on the host gut microbiome dynamics, alterations resulting from antibiotic exposure also have enduring repercussions on human health and physiological equilibrium. Therefore, enhancing gut microbiome resilience during antibiotic treatment is essential, with the goal of mitigating prolonged adverse effects. Here, we explored the impact of pre-antibiotic microbial and functional profiles on resilience, suggesting that specific baseline features exhibit greater resilience to antibiotics-induced changes. Our results identified an uncultured Faecalibacterium prausnitzii taxon as a species at baseline associated with diminished resilience. We demonstrated that this association could be linked to the role of this F. prausnitzii taxon as a keystone species. Additionally, we observed the influence of other commensal bacteria, such as Bifidobacterium animalis and Lactobacillus acidophilus, as well as functional modules, such as multidrug resistance efflux pump, on resilience. This lays the foundations for designing targeted strategies to promote a resilient gut microbiome before antibiotic treatment, alleviating possible prolonged effects on human health.

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confidence: 91%

Baseline microbiome composition impacts resilience to and recovery following antibiotics

Chen,

Löber,

Bartolomaeus

et al. 2024

Preprint

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“…These definitions and approaches could be helpful for future ecological studies aiming at answering questions related to the role and importance of the rare biosphere. Collectively, the findings presented here advance our understanding of natural microbial community response to disturbance, and thus, could be useful for ecosystem management, e.g., microbiome rescue [8] in a changing world.…”

Section: Discussionmentioning

confidence: 92%

“…Members of the rare biosphere have also been shown to become abundant in a bacterioplankton community after disturbance and play important roles in maintaining ecosystem processes [6]. Rare taxa can periodically become abundant, and their abundance dynamics may depend on selection pressure such as those imposed by seasonal fluctuations in environmental parameters and substrate availability, and/or ecological processes including dispersal, predation, reactivation from dormancy, functional redundancy, plasticity, and diversification [7,8].…”

Section: Introductionmentioning

confidence: 99%

Microbial Response to Natural Disturbances: Rare Biosphere often plays a role

Zhao,

Brandt,

Wang

et al. 2024

Preprint

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Understanding how microbial populations respond to disturbances represents a major goal for microbial ecology. While several theories have been advanced to explain microbial community compositional changes in response to disturbances, appropriate data to test these theories is scarce, especially when considering the challenges to define rare vs. abundant taxa and generalists vs. specialists, a prerequisite for testing the theories. Here, we define these two key concepts by employing the patterns of coverage of a (target) genome by a metagenome to define rare populations, and by borrowing concepts from macroecology, the proportional similarity index (PS index), to define generalists. Using these concepts, we found that coastal microbial communities are resilient to major perturbations such as tropical cyclones and (uncommon) cold or warm weather events snaps -in part- due to the response of rare populations, providing support for the insurance hypothesis (i.e., the rare biosphere has the buffering capacity to mitigate the effects of disturbances). Generalists appear to contribute proportionally more than specialists to community adaptation to perturbations like warming, supporting the disturbance-specialization hypothesis, i.e., disturbance favors generalists. Taken together, our results advance understanding of the mechanisms governing microbial populations dynamics under changing environmental conditions and have potential applications for ecosystem management.

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“…This process effectively rebuilds and accumulates the dormant "seed bank" but does not contribute immediately to functional recovery (i.e., active populations) until conditions become favorable for activity. Thus, re-establishing the microbial seed bank during or after a disturbance could provide a restoration management strategy (Moreira-Grez et al 2019;King & Bell 2022;Shade 2023). Patterns of OTU activity over time in fire-affected sites demonstrated that many bacteria are likely to be activating (either after dispersal or from the local seed bank) in the fire-affected soils over the last few years as the soils have cooled.…”

Section: Discussionmentioning

confidence: 99%

“…However, the rate and degree of resilience of these communities can vary widely. The perceived variability in resilience may be due to complex, interacting, and poorly understood ecological and evolutionary mechanisms (Shade et al 2012;Griffiths & Philippot 2013;Shade 2023), including the interplay of speciation, selection, and dispersal assembly processes (Vellend 2010;Nemergut et al 2013). Quantifications of microbiome resilience may also be complicated by the substantial pool of dormant microorganisms that persists in many environmental systems, but especially in soils (Aanderud et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Arrive and wait: inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

Barnett

Shade

2023

Preprint

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Soil microbiomes are essential mediators of ecosystem services, and their resistance and resilience to anthropogenic disturbances can have profound effects on soil function. However, we know little about the determinants of soil microbiome resilience, especially in the context of long-term (press) disturbances. Here, we leveraged the seven-decade-old underground coal seam fire in Centralia, Pennsylvania, USA, to examine surface soil bacterial community resilience to long-term heat disturbance. As the fire slowly advances along coal seams, formerly fire-affected soils cool to ambient temperature enabling geographically localized comparisons of impacted soils across a gradient of fire intensities with recovered and reference soils. To assess soil bacterial microbiome response and resilience to the fire, we executed a seven-year field study, annually sampling sites selected to capture the range of disturbance intensities. We quantified the dynamics of the bacterial communities over time and across the fire-impact gradient and additionally accounted for population activation by combining 16S rRNA with 16S rRNA gene amplicon sequencing. Over the years, the fire-affected sites cooled, and their microbiome structures recovered towards those of reference and recovered soils. However, the whole community demonstrated greater resilience than the active subset, suggesting that resilience could not solely be attributed to environmental selection and growth of active populations. We therefore suggest that regional dispersal, persistence, and revival from the local seed bank contribute to microbiome resilience. Importantly, this work indicates that DNA-based methods that do not account for activity may overestimate microbiome resilience, with implications for understanding microbiome functional recovery.

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Microbiome rescue: directing resilience of environmental microbial communities

Cited by 23 publications

References 66 publications

Baseline microbiome composition impacts resilience to and recovery following antibiotics

Baseline microbiome composition impacts resilience to and recovery following antibiotics

Microbial Response to Natural Disturbances: Rare Biosphere often plays a role

Arrive and wait: inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

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