A predictive index for health status using species-level gut microbiome profiling

Gupta, Vinod Kumar; Kim, Minsuk; Bakshi, Utpal; Cunningham, Kevin Y.; Davis, John M.; Lazaridis, Konstantinos N.; Nelson, Heidi; Chia, Nicholas; Sung, Jaeyun

doi:10.1038/s41467-020-18476-8

Cited by 144 publications

(155 citation statements)

References 67 publications

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“…6). Our microbiome signature of health showed high overlap with signatures reported in the GMHI study 51…”

Section: Definition Of Healthy and Disease-associated Gut Microbiomesupporting

confidence: 52%

“…51 The existence of shared dysbiosis has considerable implications for microbiome research and development of microbiota-targeting diagnostics and therapies. It implies that the gut microbiome is a biomarker of general health, which is supported by our prediction models and by previous studies 51,58 . However, this also complicates microbiome-based diagnosis of individual diseases because single-disease models might be confounded by signals shared across unrelated diseases, and testing such models for specificity in mixeddisease cohorts will be an important step before clinical implementation.…”

Section: Discussionmentioning

confidence: 99%

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The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

Weersma

Kurilshikov

Vila

et al. 2020

Preprint

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The gut microbiome is associated with diverse diseases, but the universal signature of an (un)healthy microbiome remains elusive and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. To fill this gap, we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We then correlated this to 241 host and environmental factors, including physical and mental health, medication use, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is primarily shaped by environment and cohousing. Only ~13% of taxa are heritable, which are enriched with highly prevalent and health-associated bacteria. By identifying 2,856 associations between microbiome and health, we find that seemingly unrelated diseases share a common signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, of which numerous early-life and current factors are particularly linked to the microbiome. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.

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“…6). Our microbiome signature of health showed high overlap with signatures reported in the GMHI study 51…”

Section: Definition Of Healthy and Disease-associated Gut Microbiomesupporting

confidence: 52%

Section: Discussionmentioning

confidence: 99%

The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

Weersma

Kurilshikov

Vila

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…4b). Finally, we calculated the recently developed Gut Microbiome Health Index (GMHI) 51 for our data and identified a significant difference in GMHI between healthy and unhealthy individuals (p-value = 1.1e-11, balanced accuracy 0.61, Supplementary fig. 6).…”

Section: Resultsmentioning

confidence: 99%

The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

Kurilshikov

Vila

Sinha

et al. 2020

Preprint

View full text Add to dashboard Cite

The gut microbiome is associated with diverse diseases, but the universal signature of an (un)healthy microbiome remains elusive and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. To fill this gap, we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We then correlated this to 241 host and environmental factors, including physical and mental health, medication use, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is primarily shaped by environment and cohousing. Only ∼13% of taxa are heritable, which are enriched with highly prevalent and health-associated bacteria. By identifying 2,856 associations between microbiome and health, we find that seemingly unrelated diseases share a common signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, of which numerous early-life and current factors are particularly linked to the microbiome. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.

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“…Increased α-diversity in adults is commonly considered to be correlating with a healthy/healthier status. However, other parameters than α-diversity seem to be better predictors for this [ 29 ], although it is unclear whether that is also the case for children, as this has been established only in adults. Also, how α-diversity in children relates to health is as yet unclear.…”

Section: Resultsmentioning

confidence: 99%

Gut microbiota profile of Indonesian stunted children and children with normal nutritional status

et al. 2021

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The gut microbiota has been shown to play a role in energy metabolism of the host. Dysbiosis of the gut microbiota may predispose to obesity on the one hand, and stunting on the other. The aim of the study was to study the difference in gut microbiota composition of stunted Indonesian children and children of normal nutritional status between 3 and 5 years. Fecal samples and anthropometric measurements, in addition to economic and hygiene status were collected from 78 stunted children and 53 children with normal nutritional status in two regions in Banten and West Java provinces: Pandeglang and Sumedang, respectively. The gut microbiota composition was determined by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. The composition was correlated to nutritional status and anthropometric parameters. Macronutrient intake was on average lower in stunted children, while energy-loss in the form of short-chain fatty acids (SCFA) and branched-chain fatty acids (BCFA) appeared to be higher in stunted children. In stunted children, at the phylum level the relative abundance of Bacteroidetes (44.4%) was significantly lower than in normal children (51.3%; p-value 2.55*10−4), while Firmicutes was significantly higher (45.7% vs. 39.8%; p-value 5.89*10−4). At the genus level, overall Prevotella 9 was the most abundant genus (average of 27%), and it was significantly lower in stunted children than in normal children (23.5% vs. 30.5%, respectively; q-value 0.059). Thirteen other genera were significantly different between stunted and normal children (q-value < 0.1), some of which were at low relative abundance and present in only a few children. Prevotella 9 positively correlated with height (in line with its higher relative abundance in normal children) and weight. In conclusion, Prevotella 9, which was the most abundant genus in the children, was significantly lower in stunted children. The abundance of Prevotella has been correlated with dietary fibre intake, which was lower in these stunted children. Since fibres are fermented by the gut microbiota into SCFA, and these SCFA are a source of energy for the host, increasing the proportion of Prevotella in stunted children may be of benefit. Whether this would prevent the occurrence of stunting or even has the potential to revert it, remains to be seen in follow up research.

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A predictive index for health status using species-level gut microbiome profiling

Cited by 144 publications

References 67 publications

The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

The Dutch Microbiome Project defines factors that shape the healthy gut microbiome

Gut microbiota profile of Indonesian stunted children and children with normal nutritional status

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