Characterizing scaling laws in gut microbial dynamics from time series data: caution is warranted

Wang, Xu‐Wen; Liu, Yang‐Yu

doi:10.1101/2021.01.11.426045

Cited by 4 publications

(4 citation statements)

References 8 publications

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“…Since the distributions of

, and

are dependent on correlations between sampling times, it was initially puzzling that their distributions in some data sets remained similar after shuffling sampling times, raising questions as to what extent these statistics hold information about the underlying intrinsic dynamics ( Tchourine et al, 2021 ; Wang and Liu, 2021a ). Our results assist in reconciling the apparent conundrum, since within our model richness

and Taylor’s law exponent

do not depend on correlations between sampling times and are also the statistics that are most informative about the intrinsic parameters

and

( Figure 3 ).…”

Section: Resultsmentioning

confidence: 99%

Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas

Good

Huang

2022

eLife

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Across diverse microbiotas, species abundances vary in time with distinctive statistical behaviors that appear to generalize across hosts, but the origins and implications of these patterns remain unclear. Here, we show that many of these macroecological patterns can be quantitatively recapitulated by a simple class of consumer-resource models, in which the metabolic capabilities of different species are randomly drawn from a common statistical distribution. Our model parametrizes the consumer-resource properties of a community using only a small number of global parameters, including the total number of resources, typical resource fluctuations over time, and the average overlap in resource-consumption profiles across species. We show that variation in these macroscopic parameters strongly affects the time series statistics generated by the model, and we identify specific sets of global parameters that can recapitulate macroecological patterns across wide-ranging microbiotas, including the human gut, saliva, and vagina, as well as mouse gut and rice, without needing to specify microscopic details of resource consumption. These findings suggest that resource competition may be a dominant driver of community dynamics. Our work unifies numerous time series patterns under a simple model, and provides an accessible framework to infer macroscopic parameters of effective resource competition from longitudinal studies of microbial communities.

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“…Since the distributions of

, and

and Taylor’s law exponent

do not depend on correlations between sampling times and are also the statistics that are most informative about the intrinsic parameters

and

( Figure 3 ).…”

Section: Resultsmentioning

confidence: 99%

Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas

Good

Huang

2022

eLife

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“…To understand the nature of those scaling laws, we introduced a null model by randomly shu✏ing the time series to destroy the temporal structure in the original time series [29]. We found that most of the scaling laws can still be observed up to the change of the exponent values (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Second, what are the underlying mechanisms responsible for those scaling laws? Recently, we found that those scaling laws can still be observed from the shu✏ed time series of the human and mouse gut microbiomes, where the temporal structure in the original time series has been largely destroyed [29]. This finding prompts us to hypothesize that temporal fluctuations might be the key to explain those scaling laws.…”

mentioning

confidence: 93%

Origins of Scaling Laws in Microbial Dynamics

Wang

Liu

2021

Preprint

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Analysis of high-resolution time series data from the human and mouse gut microbiomes revealed that the gut microbial dynamics can be characterized by several robust and simple scaling laws. It is still unknown if those scaling laws are universal across different body sites, host species, or even free-living microbial communities. Moreover, the underlying mechanisms responsible for those scaling laws remain poorly understood. Here, we demonstrate that those scaling laws are not unique to gut microbiome, but universal across different habitats, from human skin and oral microbiome to marine plankton bacteria and eukarya communities. Since completely shuffled time series yield very similar scaling laws, we conjecture that the universal scaling laws in various microbiomes are largely driven by temporal stochasticity of the host or environmental factors. We leverage a simple population dynamics model with both deterministic inter-species interactions and stochastic noise to confirm our conjecture. In particular, we find that those scaling laws are jointly determined by inter-species interactions and linear multiplicative noises. The presented results deepen our understanding of the nature of scaling laws in microbial dynamics.

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“…We are surprised by the letter by Wang and Liu 1 related to our recent study demonstrating that short- and long-term microbiota dynamics can be characterized by multiple macroecological relationships 2 . The discovery of these laws in microbiota represents an important advance in the understanding of microbial ecology.…”

Section: Figurementioning

confidence: 90%

Multiple macroecological laws do characterize various aspects of microbiota dynamics

Tchourine

Carballo-Pacheco

Vitkup

2021

Preprint

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In this letter we address the potential confusion related to our recent demonstration that multiple macroecological laws describe short- and long-term dynamics of microbial communities. Specifically, we clarify that these laws, similarly to many other relationships observed in nature, are characterized not just by the existence of scaling, but also by certain characteristic values of the scaling exponents. By performing proper statistical analysis, we demonstrate that the relationships sensitive to temporal bacterial dynamics are not reproduced in the shuffled data. We also discuss that there is no clear evidence in the data that macroecological relationships in microbiota are primarily driven by external or environmental factors. Proper statistical analyses of the data suggest that the dynamics of gut microbiota, even on a constant diet, contains rich temporal structure. Therefore, it is likely that complex and non-linear internal dynamics may be primarily responsible for the observed macroecological laws in microbiota and other ecological communities.

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Characterizing scaling laws in gut microbial dynamics from time series data: caution is warranted

Cited by 4 publications

References 8 publications

Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas

Competition for fluctuating resources reproduces statistics of species abundance over time across wide-ranging microbiotas

Origins of Scaling Laws in Microbial Dynamics

Multiple macroecological laws do characterize various aspects of microbiota dynamics

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