Microbiomes as sources of emergent host phenotypes

Lynch, Jonathan B.; Hsiao, Elaine Y.

doi:10.1126/science.aay0240

Cited by 243 publications

(161 citation statements)

References 42 publications

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“…Recent advances in microbiome research revealed that the gut microbiome is not just a passive bystander, but actively impacts multiple host functions, including circadian rhythmicity, nutritional responses, metabolism and immunity. 3,4 The mammalian immune system encompasses a complex network of innate and adaptive components in all tissues, and plays a vital role in host defense against various potentially harmful external agents and endogenous perturbations of homeostasis. From an ecological perspective, mammals and their commensal microorganisms co-evolved toward mutualism and hemostasis.…”

Section: Introductionmentioning

confidence: 99%

Interaction between microbiota and immunity in health and disease

2020

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The interplay between the commensal microbiota and the mammalian immune system development and function includes multifold interactions in homeostasis and disease. The microbiome plays critical roles in the training and development of major components of the host's innate and adaptive immune system, while the immune system orchestrates the maintenance of key features of host-microbe symbiosis. In a genetically susceptible host, imbalances in microbiota-immunity interactions under defined environmental contexts are believed to contribute to the pathogenesis of a multitude of immune-mediated disorders. Here, we review features of microbiome-immunity crosstalk and their roles in health and disease, while providing examples of molecular mechanisms orchestrating these interactions in the intestine and extra-intestinal organs. We highlight aspects of the current knowledge, challenges and limitations in achieving causal understanding of host immune-microbiome interactions, as well as their impact on immune-mediated diseases, and discuss how these insights may translate towards future development of microbiometargeted therapeutic interventions.

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Section: Introductionmentioning

confidence: 99%

Interaction between microbiota and immunity in health and disease

2020

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“…Gut microbiota take part in many functional metabolic pathways to in uence nutrient digestion and absorption, lipid metabolism and hormone biosynthesis. These can, in turn, affect host behaviors such as social communication, stress response, cognition and feeding behavior [39]. Thus, we further analyzed the functional pathway enrichment to predict the in uence of the early social contact on the gut microbial functions of piglets.…”

Section: Discussionmentioning

confidence: 99%

The effect of early social contact on the community structure and functions of fecal microbiome in suckling - growing piglets

Liu

et al. 2020

Preprint

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Background: Social contact in the early suckling period as an enriched social environment can reduce the aggressive behaviors of piglets at weaning regrouping, and improve their production performance and welfare. We speculated that the social environment could modulate the maturation of piglet intestinal microbiota at later growth stages. Therefore, we performed microbial 16S rRNA gene sequencing from fecal samples, collected at 16, 35, 42, and 63 days of age, to investigate the structure and function of intestinal microbiota in piglets that experienced early social contact. Results: The results showed that the litter weight of the piglets was not significantly different between the control (CON) and social contact (SC) groups at 35 days of age (P > 0.05), but the weight of piglets in the SC group significantly decreased at 63 days compared to the CON group (P < 0.05). While the proportion of Firmicutes were the most abundant bacterial phylum detected in both groups at all times, the proportion of Firmicutes and the Firmicutes-to-Bacteroides ratio were significantly higher in the SC group compared to the CON group and the proportion of Bacteroides was lower in the SC group compared to the CON group at 35, 42, and 63 days of age (P < 0.05). At the genus level, early social contact had a significant positive effect on the level of Lactobacillus at 35 and 42 days of age (P < 0.05), but a negative effect on Prevotella at 35, 42, and 63 days of age (P < 0.05). Furthermore, functional analysis of the microbial composition showed that the changes induced by early social contact mainly altered the relative abundance of metabolic and related pathways. From 35 days of age, the social contact notably had a negative effect on the abundance microbial pathways for protein digestion and absorption and lipid metabolism (P < 0.05). Conclusions: Early social contact truly changed the taxonomy of fecal microbiota in piglets, which in turn, impacted the potential for microbial function within the piglet intestine. At present, we speculate that providing continuous social contact negatively influences the nutrient metabolism for the growing piglets.

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“…Investigations into human gut microbiome has revealed the pivotal role of microbial communities in host health and disease 1 , however the majority of the studied microbiome are from defecated feces, which are powerful representations of gastrointestinal (GI) microbial ecosystems yet still with limitations. Fecal microbiome largely represent the last stage of transitions of microbial communities along the GI tract, and as numerous biogeographical analyses revealed the distinction of fecal microbiome from different GI sections 2 , where important biological processes take place.…”

Section: Introductionmentioning

confidence: 99%

Reconstruction and dynamics of human intestinal microbiome observedin situ

Liu

Dai

et al. 2020

Preprint

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45Gut microbiome are studied primarily using fecal samples in humans and we gained 46 vital knowledge of compositional and functional capacities of gastro-intestinal 47 microbial communities. Yet, fecal materials limit our ability to investigate microbial 48 dynamics in different locations along GI-tract (in situ), nor in finer temporal scales as 49 they are infrequent. With a technology developed originally for fecal material 50 transplantation, colonic transendoscopic enteral tubing, we were able to sample 51 ileocecal microbiome twice daily, and carried out metagenomic as well as 52 metatranscriptomic analyses. Ileocecal and fecal microbiome are similar in 53 metagenomic profiling, yet their active genes (in metatranscriptomes) are highly 54 distinct. Both were perturbed after laxatives and then became more similar to 55 microbiome prior to treatment, demonstrating resilience as an innate property of gut 56 microbiome. Ileocecal microbiome transcriptomes sampled during day and night 57 revealed diurnal rhythmes exist in certain bacterial species and functional pathways, in 58 particular those related to short-chain fatty acid production. Lastly, metabolomic 59 analysis in fecal and urine samples mirrored the perturbance and recovery in gut 60 microbiome, indicating crucial contribution of gut microbiome to many of the key 61 metabolites involved in host health. Our study provides interesting novel insights into 62 human gut microbiome, and demonstrates the inner resilience, diurnal rhythmes and 63 potential consequences to the host. 64 65 66 (Figure 1, Figure S1). Yet those microbial species do not always occupy the majority 131 in RNA reads, rather, species Ruminococcus torques, Methanobrevibacter, 132

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Microbiomes as sources of emergent host phenotypes

Cited by 243 publications

References 42 publications

Interaction between microbiota and immunity in health and disease

Interaction between microbiota and immunity in health and disease

The effect of early social contact on the community structure and functions of fecal microbiome in suckling - growing piglets

Reconstruction and dynamics of human intestinal microbiome observedin situ

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