Conceptual strategies for characterizing interactions in microbial communities

Kodera, Sho M.; P, Dás; Gilbert, Jack A.; Lutz, Holly L.

doi:10.1016/j.isci.2022.103775

Cited by 27 publications

(18 citation statements)

References 112 publications

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“…To further understand whether the long-term antibiotic treatments induce the network remodeling of the gut microbiota, we performed SparCC co-occurrence network analyses to determine the interactive complexity of bacteria in the microbiota by the number of nodes and edges. 30 We found that although the number of nodes (genus-level taxa) was similar between untreated microbiota (node number = 98) and short-term treated microbiota (node number = 95), the edge number of the short-term treated microbiota was decreased from 399 to 168 ( Figure 3A and B ). Higher modularity was also observed in the short-term treated network, suggesting that the antibiotic treatment disrupted the compact network connections observed in untreated microbiota ( Figure 3B ).…”

Section: Resultsmentioning

confidence: 89%

The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling

Chen

Lin

et al. 2023

Bioinform Biol Insights

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Antibiotic treatment has been shown to cause gut microbiota dysbiosis. However, lacking critical features defining gut microbiota dysbiosis makes it challenging to prevent. By co-occurrence network analysis, we found that despite short antibiotic courses eliminating certain microbial taxa, the Akkermansia genus played the role of a high-centrality hub to maintain microbiota homeostasis. When the antibiotic courses continued, the elimination of Akkermansia induced a significant microbiota remodeling of the gut microbiota networks. Based on this finding, we found that under long-term antibiotic stress, the gut microbiota was rearranged into a stable network with a significantly lower Akkermansiaceae/ Lachnospiraceae (A/L) ratio and no microbial hub. By functional prediction analysis, we confirmed that the gut microbiota with a low A/L ratio also had enhanced mobile elements and biofilm-formation functions that may be associated with antibiotic resistance. This study identified A/L ratio as an indicator of antibiotic-induced dysbiosis. This work reveals that besides the abundance of specific probiotics, the hierarchical structure also critically impacts the microbiome function. Co-occurrence analysis may help better monitor the microbiome dynamics than only comparing the differentially abundant bacteria between samples.

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Section: Resultsmentioning

confidence: 89%

The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling

Chen

Lin

et al. 2023

Bioinform Biol Insights

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“…Pairwise interactions are frequently assumed in constructing dynamical systems models of ecological systems [1][2][3][4]. This is a foundational assumption of classical evolutionary game theory in which the replicator dynamic is built from a matrix game [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Higher Order Dynamics in the Replicator Equation Produce a Limit Cycle in Rock-Paper-Scissors

Griffin¹,

Wu²

2023

Preprint

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Recent work has shown that pairwise interactions may not be sufficient to fully model ecological dynamics in the wild. In this letter, we consider a replicator dynamic that takes both pairwise and triadic interactions into consideration using a rank three tensor. We study this new nonlinear dynamics using a generalised rock-paper-scissors game whose dynamics are well understood in the classic replicator sense. We show that the addition of higher-order dynamics leads to the creation of a subcritical Hopf bifurcation and consequently an unstable limit cycle. It is known that this kind of behaviour cannot occur in the pairwise replicator in any three strategy games, showing the effect higher-order interactions can have on the resulting dynamics of the system. We numerically characterise parameter regimes in which limit cycles exist and discuss possible ways to generalise this approach to studying higher-order interactions.

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“…Furthermore, culture-based methods do not capture changes in the ecological structure of the community as a whole, which can provide valuable insights into ecosystem health [ 10 , 46 , 47 ]. Bacterial pathogens and fecal indicator taxa do not exist in isolation, rather, they exist within expansive, interactive communities of diverse and abundant microbial members [ 12 , 24 ]. Therefore, improving our understanding of the relationship between microbiology and water quality may require a more holistic examination of the microbial community.…”

Section: Introductionmentioning

confidence: 99%

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

Kodera

Sharma

Martino

et al. 2023

Environmental Microbiome

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Background Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013–2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. Results Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. Conclusions This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

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Conceptual strategies for characterizing interactions in microbial communities

Cited by 27 publications

References 112 publications

The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling

The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling

Higher Order Dynamics in the Replicator Equation Produce a Limit Cycle in Rock-Paper-Scissors

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

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