Co-existence of Network Architectures Supporting the Human Gut Microbiome

Hall, Caitlin; Lord, Anton; Betzel, Richard F.; Zakrzewski, Martha; Simms, Lisa A.; Zalesky, Andrew; Radford‐Smith, Graham; Cocchi, Luca

doi:10.1016/j.isci.2019.11.032

Cited by 35 publications

(27 citation statements)

References 36 publications

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“…These module clusters may be indicative of niches that are retained in the healthy human gut microbiome, and the redundancy of multiple modules of a cohort falling within a cluster is potentially a further stabilizing force for the ecosystem. These findings agree with previous studies showing comparable communities and high functional redundancy across gut microbiome data sets 55 , 67 .…”

Section: Discussionsupporting

confidence: 93%

Bacterial associations in the healthy human gut microbiome across populations

Loftus

Hassouneh

Yooseph

2021

Sci Rep

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In a microbial community, associations between constituent members play an important role in determining the overall structure and function of the community. The human gut microbiome is believed to play an integral role in host health and disease. To understand the nature of bacterial associations at the species level in healthy human gut microbiomes, we analyzed previously published collections of whole-genome shotgun sequence data, totaling over 1.6 Tbp, generated from 606 fecal samples obtained from four different healthy human populations. Using a Random Forest Classifier, we identified 202 signature bacterial species that were prevalent in these populations and whose relative abundances could be used to accurately distinguish between the populations. Bacterial association networks were constructed with these signature species using an approach based on the graphical lasso. Network analysis revealed conserved bacterial associations across populations and a dominance of positive associations over negative associations, with this dominance being driven by associations between species that are closely related either taxonomically or functionally. Bacterial species that form network modules, and species that constitute hubs and bottlenecks, were also identified. Functional analysis using protein families suggests that much of the taxonomic variation across human populations does not foment substantial functional or structural differences.

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Section: Discussionsupporting

confidence: 93%

Bacterial associations in the healthy human gut microbiome across populations

Loftus

Hassouneh

Yooseph

2021

Sci Rep

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“…We finally applied our method to infer microbial association networks from real-world taxonomic profiles generated from healthy gut microbiomes of the LifeLines-Deep [32] population cohort ( n =1135) (using the metapalette software [33]). Even though confirmed ecological interactions within natural microbial communities are only scarcely known, several global network properties have been reproducibly documented, including the salient observation of preferential associations among phylogenetically close organisms [35, 36]. This property, known as assortativity, is manifest at the level of highly connected components in our analysis, and is displayed for the species taxonomic level in Figure 4.…”

Section: Resultsmentioning

confidence: 78%

A zero inflated log-normal model for inference of sparse microbial association networks

Prost

Gazut

Brüls

2020

Preprint

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The advent of high-throughput metagenomic sequencing has prompted the development of efficient taxonomic profiling methods allowing to measure the presence, abundance and phylogeny of organisms in a wide range of environmental samples. Multivariate sequence-derived abundance data further has the potential to enable inference of ecological associations between microbial populations, but several technical issues need to be accounted for, like the compositional nature of the data, its extreme sparsity and overdispersion, as well as the frequent need to operate in under-determined regimes.The ecological network reconstruction problem is frequently cast into the paradigm of Gaussian graphical models (GGMs) for which efficient structure inference algorithms are available, like the graphical lasso and neighborhood selection. Unfortunately, GGMs or variants thereof can not properly account for the extremely sparse patterns occurring in real-world metagenomic taxonomic profiles. In particular, structural zeros (as opposed to sampling zeros) corresponding to true absences of biological signals fail to be properly handled by most statistical methods.We present here a zero-inflated log-normal graphical model specifically aimed at handling such “biological” zeros, and demonstrate significant performance gains over state-of-the-art statistical methods for the inference of microbial association networks, with most notable gains obtained when analyzing taxonomic profiles displaying sparsity levels on par with real-world metagenomic datasets.

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“…By T3, the overall taxonomic network connectivity was formed exclusively from rare OTUs. Contrastingly, abundant OTUs were peripherals and disconnected from central hubs [60], mainly composed of putative opportunistic invaders such as Mycoplasma and other genera encompassing strains associated to sh pathogens, like Bacillus (>6% in CC and CV). As observed in other sh species such as Atlantic salmon (Salmo salar) [77] and the long jaw mudsucker (Gillichythys mirabilis) [78,79], Yellow Perch have intestinal micro ora dominated by Tenericutes (Mycoplasma sp.).…”

Section: Discussionmentioning

confidence: 95%

“…Within gut microbial communities, the high abundant OTUs are peripheral (with minimal interactions) or disassortative (not connected) to the giant network component, see [60], suggesting low overall connectivity ( Figure 2D ). Within skin and gut microbiome networks, no correlation was found between the degree (number of connections per node) and the average relative abundance of OTUs (nodes size in the network).…”

Section: Substantial Role Of Rare Taxa In Microbiome Network Connectimentioning

confidence: 99%

The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance

Cheaib

Seghouani

Llewellyn

et al. 2020

Preprint

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Background: Disentangling the dynamics of microbial interactions within communities improves our comprehension of metacommunity assembly of microbiota during host development and under perturbations. To assess the impact of stochastic variation of neutral processes on microbiota structure and composition under disturbance, two types of microbial habitats, free-living (water), and host-associated (skin and gut) were experimentally exposed to either a constant or gradual selection regime exerted by two sublethal cadmium chloride dosages (CdCl2). Yellow Perch (Perca flavescens) was used as a piscivorous ecotoxicological model. Using 16S rDNA gene based metataxonomics, quantitative diversity metrics of water, skin and gut microbial communities were characterized along with development and across experimental conditions. Results: After 30 days, constant and gradual selection regimes drove a significant alpha diversity increase for both skin and gut microbiota. In the skin, pervasive negative correlations between taxa in both selection regimes in addition to the taxonomic convergence with the environmental bacterial community, suggest a loss of colonisation resistance resulting in the dysbiosis of yellow perch microbiota. Furthermore, the network connectivity in gut microbiome was exclusively maintained by rare (low abundance) OTUs, while most abundant OTUs were mainly composed of opportunistic invaders such as Mycoplasma and other genera related to fish pathogens such as Flavobacterium. Finally, the mathematical modelling of community assembly using both non-linear least squares models (NLS) based estimates of migration rates and normalized stochasticity ratios (NST) based beta-diversity distances suggested neutral processes drove by taxonomic drift in host and water communities for almost all treatments. The NLS models predicted higher demographic stochasticity in the cadmium-free host and water microbiomes, however, NST models suggested higher ecological stochasticity under perturbations. Conclusions: Neutral models agree that water and host-microbiota assembly promoted by rare taxa have evolved predominantly under neutral processes with potential involvement of deterministic forces sourced from host filtering and cadmium selection. The early signals of perturbations in the skin microbiome revealed antagonistic interactions by a preponderance of negative correlations in the co-abundance networks. Our findings enhance our understanding of community assembly host-associated and free-living under anthropogenic selective pressure.

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Co-existence of Network Architectures Supporting the Human Gut Microbiome

Cited by 35 publications

References 36 publications

Bacterial associations in the healthy human gut microbiome across populations

Bacterial associations in the healthy human gut microbiome across populations

A zero inflated log-normal model for inference of sparse microbial association networks

The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance

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