Species-level functional profiling of metagenomes and metatranscriptomes

Franzosa, Eric A.; McIver, Lauren J.; Rahnavard, Ali; Thompson, Luke R.; Schirmer, Melanie; Weingart, George; Lipson, Karen Schwarzberg; Knight, Rob; Caporaso, J. Gregory; Segata, Nicola; Huttenhower, Curtis

doi:10.1038/s41592-018-0176-y

Cited by 1,193 publications

(1,104 citation statements)

References 52 publications

Supporting

Mentioning

1,097

Contrasting

Unclassified

Order By: Relevance

“…Mean nearest sequenced taxon index = 0.12 6 0.02. Microbial pathways were profiled with HUMAnN2 (33), and comparison of the pathways overrepresented in RS compared with NS microbial communities was performed with linear discriminant analysis effect size (LEfSe) (34). Metabolic pathways with a linear discriminant analysis score .2 were considered significant.…”

Section: Microbiome Analysismentioning

confidence: 99%

Ingestion of resistant starch by mice markedly increases microbiome‐derived metabolites

et al. 2019

View full text Add to dashboard Cite

Recent research has shown significant health benefits deriving from high‐dietary fiber or microbiome‐accessible carbohydrate consumption. Compared with native starch (NS), dietary resistant starch (RS) is a high microbiome‐accessible carbohydrate that significantly alters the gut microbiome. The aim of this study was to determine the systemic metabolic effects of high microbiome‐accessible carbohydrate. Male C57BL/6 mice were divided into 2 groups and fed either NS or RS for 18 wk (n = 20/group). Metabolomic analyses revealed that plasma levels of numerous metabolites were significantly different between the RS‐fed and NS‐fed mice, many of which are microbiome‐derived. Most strikingly, we observed a 22‐fold increase in gut microbiome‐derived tryptophan metabolite indole‐3‐propionate (IPA), which was positively correlated with several gut microbiota, including Allobaculum, Bifidobacterium, and Lachnospiraceae, with Allobaculum having the most consistently increased abundance of all the IPA‐associated taxa across all RS‐fed mice. In addition, major changes were observed for metabolites solely or primarily metabolized in the gut (e.g., trimethylamine‐N‐oxide), metabolites that have a significant entero‐hepatic circulation (i.e., bile acids), lipid metabolites (e.g., cholesterol sulfate), metabolites indicating increased energy turnover (e.g., tricarboxylic acid cycle intermediates and ketone bodies), and increased antioxidants such as reduced glutathione. Our findings reveal potentially novel mediators of high microbiome‐accessible carbohydrate‐derived health benefits.—Koay,Y. C., Wali. J. A., Luk, A. W. S., Macia, L., Cogger, V. C., Pulpitel, T. J., Wahl, D., Solon‐Biet, S. M., Holmes, A., Simpson, S. J., O'Sullivan, J. F. Ingestion of resistant starch by mice markedly increases microbiome‐derived metabolites. FASEB J. 33, 8033–8042 (2019). http://www.fasebj.org

show abstract

Section: Microbiome Analysismentioning

confidence: 99%

Ingestion of resistant starch by mice markedly increases microbiome‐derived metabolites

et al. 2019

View full text Add to dashboard Cite

show abstract

“…To complement our optimized taxa-based approach and further utilize the resolution afforded by shotgun metagenomic sequencing, we applied HUMANn2 to identify the functional potential of microbial pathways present in the MI samples (Franzosa et al, 2018) [Table S4]. Utilizing both the Kraken2/GTDB and HUMANn2 pipelines, we identified a broad range of diversity across the 946 individuals in this geographically-restricted cohort of healthy French adults.…”

Section: Variable Gut Microbiomes In a Restricted Geographical Regionmentioning

confidence: 99%

Stability and dynamics of the human gut microbiome and its association with systemic immune traits

Byrd¹,

Liu

Fujimura³

et al. 2020

Preprint

View full text Add to dashboard Cite

Analysis of 1,363 deeply sequenced gut microbiome samples from 946 healthy donors of the Milieu Intérieur cohort provides new opportunities to discover how the gut microbiome is associated with host factors and lifestyle parameters. Using a genomebased taxonomy to achieve higher resolution analysis, we found an enrichment of Prevotella species in males, and that bacterial profiles are dynamic across five decades of life (20-69), with Bacteroidota species consistently increased with age while Actinobacteriota species, including Bifidobacterium, decreased. Longitudinal sampling revealed short-term stability exceeds inter-individual differences; however, the degree of stability was variable between donors and influenced by their baseline community composition. We then integrated the microbiome results with systemic immunophenotypes to show that host/microbe associations discovered in animal models, such as T regulatory cells and short chain fatty acids, could be validated in human data.These results will enable personalized medicine approaches for microbial therapeutics and biomarkers. ¶ unless otherwise indicated, partners are located at

show abstract

“…Such approaches are useful insofar as the presence of individual metabolic functions link directly to health or disease in the host, but this may not often be the case. Other studies are now profiling both microbiome taxonomic and functional composition to uncover patterns that may be important for health and disease in humans (Franzosa et al, ; Manor & Borenstein, ). Such methods have not yet been applied widely to plant and animal microbiomes, but most likely can and will be in the near future.…”

Section: Introductionmentioning

confidence: 99%

“…Other studies are now profiling both microbiome taxonomic and functional composition to uncover patterns that may be important for health and disease in humans (Franzosa et al, 2018;Manor & Borenstein, 2017). Such methods have not yet been applied widely to plant and animal microbiomes, but most likely can and will be in the near future.…”

Section: Introductionmentioning

confidence: 99%

Conserving the holobiont

et al. 2020

View full text Add to dashboard Cite

Organismal biology has undergone a dramatic paradigm shift in the last decade. The realization that host cells and genes are outnumbered by symbiotic microbial cells and their genes has forced us to rethink our focus on ‘individuals’. It is also becoming increasingly clear that the ecology and biology of animals and plants are intimately connected with their microbial partners. In the context of conserving functioning species, such revelatory insights beg the question—what exactly should we be trying to conserve? Here, we review how an understanding of host–microbe interactions can benefit conservation biology. We propose a way forward for conservation biologists, to gather evidence of the potential effects of changes to plant and animal microbiomes, and to incorporate the holobiont concept into applied conservation practice. In humans, microbes influence physiology, health, behaviour and psychology. In animals and plants, microbes similarly influence critically important components of health, communication and (in animals) behaviour. Together, the animal or plant and all of its associated micro‐organisms are termed the holobiont. At the same time, humans are now the strongest evolutionary force on the planet, causing global change at unprecedented scale. We know that microbial diversity in humans has been compromised in urban societies, with a growing list of consequences for health and function. While we still have limited evidence for similar effects in plants and animals, anthropogenic factors that affect diversity are also likely to affect animal and plant microbiomes, with similar associated effects on host function and health. Microbiome research is still in its relative infancy, particularly in its application to plants and animals, yet the tools are becoming more widely available and affordable. Forward‐looking conservation biologists could harness such tools and apply them to the study of plant and animal microbiomes with the goal of understanding which microbiota might be required to ensure future viability of conserved host populations. For now, the precautionary principle applies. We suggest that, to meaningfully and effectively conserve a species, we must also consider how to conserve the bacteria, viruses, fungi and other symbionts intimately associated with that macro‐organism. A free Plain Language Summary can be found within the Supporting Information of this article.

show abstract

Species-level functional profiling of metagenomes and metatranscriptomes

Cited by 1,193 publications

References 52 publications

Ingestion of resistant starch by mice markedly increases microbiome‐derived metabolites

Ingestion of resistant starch by mice markedly increases microbiome‐derived metabolites

Stability and dynamics of the human gut microbiome and its association with systemic immune traits

Conserving the holobiont

Contact Info

Product

Resources

About