Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics

Aranda-Díaz, Andrés; Willis, Lisa; Nguyen, Taylor H.; Ho, Po-Yi; Vila, Jean C. C.; Thomsen, Tani; Chavez, Taylor; Yan, Rose; Yu, Feiqiao Brian; Neff, Norma; Sánchez, Álvaro; Estrela, Sylvie; Huang, Kerwyn Casey

doi:10.1101/2023.01.13.523996

Cited by 15 publications

(15 citation statements)

References 45 publications

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“…The gut microbiota can also participate in cross-feeding, where metabolic intermediates (such as acetate, lactate, succinate and formate) that are produced by gut commensals can act as nutrients to support the growth of other gut commensals [20,21]. For example, members of the Bacteroidota and Negativicutes can convert succinate into propionate [22,23].…”

Section: Role Of the Gut Microbiota In The Metabolism Of Dietary Subs...mentioning

confidence: 99%

Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization

et al. 2023

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The human gut microbiota can restrict the growth of pathogens to prevent them from colonizing the intestine (‘colonization resistance’). However, antibiotic treatment can kill members of the gut microbiota (‘gut commensals’) and reduce competition for nutrients, making these nutrients available to support the growth of pathogens. This disturbance can lead to the growth and expansion of pathogens within the intestine (including antibiotic-resistant pathogens), where these pathogens can exploit the absence of competitors and the nutrient-enriched gut environment. In this review, we discuss nutrient competition between the gut microbiota and pathogens. We also provide an overview of how nutrient competition can be harnessed to support the design of next-generation microbiome therapeutics to restrict the growth of pathogens and prevent the development of invasive infections.

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Section: Role Of the Gut Microbiota In The Metabolism Of Dietary Subs...mentioning

confidence: 99%

Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization

et al. 2023

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“…Representatives of 17 families were reliably detected (>10 -3 abundance) in the stool inoculum and 9-18 families were detected in the three SI inocula. Yield, as assessed by optical density, varied by <2-fold across all in vitro communities, indicating that relative abundances could be at least approximately compared across communities 23 .…”

Section: In Vitro Culturing Of Human Intestinal Contents Generates St...mentioning

confidence: 97%

Improved mouse models of the small intestine microbiota using region-specific sampling from humans

Culver,

Spencer,

Violette

et al. 2024

Preprint

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Our understanding of region-specific microbial function within the gut is limited due to reliance on stool. Using a recently developed capsule device, we exploit regional sampling from the human intestines to develop models for interrogating small intestine (SI) microbiota composition and function. In vitro culturing of human intestinal contents produced stable, representative communities that robustly colonize the SI of germ-free mice. During mouse colonization, the combination of SI and stool microbes altered gut microbiota composition, functional capacity, and response to diet, resulting in increased diversity and reproducibility of SI colonization relative to stool microbes alone. Using a diverse strain library representative of the human SI microbiota, we constructed defined communities with taxa that largely exhibited the expected regional preferences. Response to a fiber-deficient diet was region-specific and reflected strain-specific fiber-processing and host mucus-degrading capabilities, suggesting that dietary fiber is critical for maintaining SI microbiota homeostasis. These tools should advance mechanistic modeling of the human SI microbiota and its role in disease and dietary responses.

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“…bacteria 7 , archaea 8 , microbial eukaryotes 9,10 ) are thought to depend on the physicochemical conditions prevailing in their habitat 11,12 , inherent growth characteristics of the inhabiting species 13 , and dynamic interspecific interactions that emerge from shared nutrient and spatial niches 14,15 . However, most of our understanding of interspecific interactions comes from experimental studies using macro-habitats, controlled growth conditions and large population census (>10 6 cells per mL) 13,[16][17][18] , which are not necessarily representative for typically highly heterogenous natural microbial habitats (e.g. soil, plant leaves, skin).…”

Section: Introductionmentioning

confidence: 99%

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Batsch,

Guex,

Todorov

et al. 2024

Preprint

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Bacteria in nature often proliferate in highly patchy environments, such as soil pores, particles, plant roots or leaves. The resulting spatial fragmentation leads to cells being constrained to smaller habitats, shared with potentially fewer other species. The effects of microhabitats on the emergence of bacterial interspecific interactions are poorly understood, but potentially important for the maintenance of diversity at a larger scale. To study this more in-depth, we contrasted paired species-growth in picoliter droplets at low population census with that in large (macro) population liquid suspended cultures. Four interaction scenarios were imposed by using different bacterial strain combinations and media: substrate competition, substrate independence, growth inhibition, and cell killing by tailocins. In contrast to macro-level culturing, we observed that fragmented growth in picoliter droplets in all cases yielded more variable outcomes, and even reversing the macro-level assumed interaction type in a small proportion of droplet habitats. Timelapse imaging and mathematical simulations indicated that the variable and alternative interaction outcomes are a consequence of founder cell phenotypic variation and small founder population sizes. Simulations further suggested that increased growth kinetic variation may be a crucial selectable property for slower-growing bacterial species to survive competition. Our results thus demonstrate how microhabitat fragmentation enables the proliferation of alternative interaction trajectories and contributes to the maintenance of higher species diversity under substrate competition.

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Assembly of gut-derived bacterial communities follows “early-bird” resource utilization dynamics

Cited by 15 publications

References 45 publications

Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization

Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization

Improved mouse models of the small intestine microbiota using region-specific sampling from humans

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

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