Fluctuation spectra of large random dynamical systems reveal hidden structure in ecological networks

Krumbeck, Yvonne; Yang, Qian; Constable, George W. A.; Rogers, Tim

doi:10.1038/s41467-021-23757-x

Cited by 16 publications

(15 citation statements)

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“…The regulatory effects of gut microbiota on enteritis, cardiovascular disease, fecal microbiota transplants, and the subsequent interactions with host genes are well-studied. However, it is a challenge to discern general principles explaining the diversity and dynamics of complex multi-species communities, since detailed biological parameters are not typically available in large ecological networks (Krumbeck et al, 2021 ). As the body is a complicated system, the regulatory mechanism of the gut microbiota on the RFI also presents a systematic coexistence and a tunable interactive effect, as shown in Figures 3 , 4 .…”

Section: Discussionmentioning

confidence: 99%

Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks

et al. 2023

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IntroductionThe objective of this study was to determine the regulatory effects of gut microbiota on the feed efficiency (FE) of small-sized meat ducks by evaluating correlations between gut microbiota and residual feed intake (RFI).MethodsA total of 500 21-day-old healthy male ducks with similar initial body weights (645 ± 15.0 g) were raised contemporaneously in the same experimental facility until slaughter at 56 days of age. In total, nine low-RFI (LR) and nine high-RFI (HR) birds were selected for further gut microbiota composition and functional analyses based on the production performance, and the RFI was calculated from 22 to 56 days of age.ResultsGrowth performance results indicated a significantly lower RFI, feed conversion ratio, feed intake, and average daily feed intake in the LR ducks (P < 0.05). Taxonomy results of gut microbiota showed the identification of 19 kinds of phyla and more than 250 kinds of genera in all samples. No significant discrepancies in cecal bacterial α-diversity were discovered between the LR and HR groups, which indicated that the microbial modulatory effects on RFI may be attributed to the bacterial composition, rather than the species diversity. Differential analysis of bacterial communities between the LR and HR groups showed a significant increment of Firmicutes and a significant decline of Bacteroidetes in the LR group (P < 0.05). Specifically, genera of Erysipelatoclostridium, Parasutterella, Fournierella, and Lactococcus significantly proliferated, while Bacteroides significantly decreased in the LR group (P < 0.05). Furthermore, correlation analysis showed that the RFI was significantly correlated with carbohydrate metabolism-related bacteria including Bacteroides, Alistipes, Bifidobacterium, Ruminiclostridium_9, Sellimonas, Oscillibacter, Escherichia-Shigella, Lactococcus, and Streptococcus.ConclusionIn conclusion, the communities related to carbohydrate metabolism had positive regulatory effects on the FE of small-sized meat ducks, promoting it by improving the relative abundance and utilization of these communities. The present study provides valuable insight into the dynamics of gut microbiota underlying the variations in the FE of small-sized meat ducks.

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Section: Discussionmentioning

confidence: 99%

Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks

et al. 2023

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“…But even without abandoning the notions of stationarity or equilibria, we could expand our formalism to address the time-scale dependency of collectivity. A way forward may be the study of power-spectra of ecological time-series: decomposing the temporal fluctuations of populations over various times scales to infer the interaction structures that generate such signals (Krumbeck et al ., 2021). Here we suspect that variations over longer time scale reflect the collective nature of communities more than those at much shorter time scales, as the latter would not allow for indirect interactions to manifest, as already illustrated by the results shown in Fig.…”

Section: Perspectivesmentioning

confidence: 99%

How collectively integrated are ecological communities?

Zelnik

Galiana

Barbier

et al. 2022

Preprint

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Are the population dynamics of species mainly determined by direct interactions with predators, preys and conspecifics? Or, instead, are those dynamics more dependent on indirect feedbacks that ripple across the whole interaction network? Here we show that, from a basic spectral feature of the interaction network, we can predict the length of indirect interaction pathways that contribute to community-level dynamical patterns, such as the depth of a perturbation's reach, or the contribution of biotic processes to realized species niches. In doing so, we propose a measure of collectivity that integrates existing approaches to community complexity, collective integration and indirect interactions. By revisiting classic concepts of theoretical community ecology, our work proposes an original perspective on the question of to what degree communities are more than loose collections of species or simple interaction motifs. This perspective can help clarify when reductionist approaches, focusing on particular species and small interaction motifs, ought to suffice or fail when applied to ecosystems.

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“…After changing the integration variables from φ to y k ≡ (φ, e k ) (an orthogonal change of variables with a unit Jacobian), the N integrations decouple into one-dimensional Gaussian (more precisely, Fresnel) integrals, and then ( 62) is recovered due to det M = k μ k and M −1 kl = n (e n ) k (e n ) l /μ n . We cannot apply (62) for cases when M is proportional to the graph Laplacian L defined by (3), since in that case M possesses a null eigenvector e 1 = (1, 1, . .…”

Section: Appendix a Pedagogical Account Of The Resistance Distancementioning

confidence: 99%

Resistance distance distribution in large sparse random graphs

Akara-pipattana¹,

Chotibut²,

Evnin³

2022

J. Stat. Mech.

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We consider an Erdős–Rényi random graph consisting of N vertices connected by randomly and independently drawing an edge between every pair of them with probability c/N so that at N → ∞ one obtains a graph of finite mean degree c. In this regime, we study the distribution of resistance distances between the vertices of this graph and develop an auxiliary field representation for this quantity in the spirit of statistical field theory. Using this representation, a saddle point evaluation of the resistance distance distribution is possible at N → ∞ in terms of an 1/c expansion. The leading order of this expansion captures the results of numerical simulations very well down to rather small values of c; for example, it recovers the empirical distribution at c = 4 or 6 with an overlap of around 90%. At large values of c, the distribution tends to a Gaussian of mean 2/c and standard deviation 2 / c 3 . At small values of c, the distribution is skewed toward larger values, as captured by our saddle point analysis, and many fine features appear in addition to the main peak, including subleading peaks that can be traced back to resistance distances between vertices of specific low degrees and the rest of the graph. We develop a more refined saddle point scheme that extracts the corresponding degree-differentiated resistance distance distributions. We then use this approach to recover analytically the most apparent of the subleading peaks that originates from vertices of degree 1. Rather intuitively, this subleading peak turns out to be a copy of the main peak, shifted by one unit of resistance distance and scaled down by the probability for a vertex to have degree 1. We comment on a possible lack of smoothness in the true N → ∞ distribution suggested by the numerics.

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Fluctuation spectra of large random dynamical systems reveal hidden structure in ecological networks

Cited by 16 publications

References 50 publications

Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks

Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks

How collectively integrated are ecological communities?

Resistance distance distribution in large sparse random graphs

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