Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents

By Christian Hoffmann, S. Dollive, Stephanie Grunberg, Jun Chen, Hongzhe Li, Gary D. Wu, James D. Lewis, Frederic D. Bushman. PLoS ONE, 2013

752 citations recorded by the source corpus.

Diet influences health as a source of nutrients and toxins, and by shaping the composition of resident microbial populations. Previous studies have begun to map out associations between diet and the bacteria and viruses of the human gut microbiome. Here we investigate associations of diet with fungal and archaeal populations, taking advantage of samples from 98 well-characterized individuals. Diet was quantified using inventories scoring both long-term and recent diet, and archaea and fungi were characterized by deep sequencing of marker genes in DNA purified from stool. For fungi, we found 66 genera, with generally mutually exclusive presence of either the phyla Ascomycota or Basiodiomycota. For archaea, Methanobrevibacter was the most prevalent genus, present in 30% of samples. Several other archaeal genera were detected in lower abundance and frequency. Myriad associations were detected for fungi and archaea with diet, with each other, and with bacterial lineages. Methanobrevibacter and Candida were positively associated with diets high in carbohydrates, but negatively with diets high in amino acids, protein, and fatty acids. A previous study emphasized that bacterial population structure was associated primarily with long-term diet, but high Candida abundance was most strongly associated with the recent consumption of carbohydrates. Methobrevibacter abundance was associated with both long term and recent consumption of carbohydrates. These results confirm earlier targeted studies and provide a host of new associations to consider in modeling the effects of diet on the gut microbiome and human health.

Subfields: Food Science, Molecular Biology, Public Health, Environmental and Occupational Health

View Paper: https://www.semanticscholar.org/paper/fb1cad1515f39da54b258fd18adada3709d50be4

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Food Science

In Molecular Biology

In Public Health, Environmental and Occupational Health

Citations in the corpus

Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome. (2019, background): “Instead, it seems that the metabolic cost of resistance leads to slower growth of bacteria, while the generally lower efficiency of generalist phages toward a particular host prevents them from taking over the specialists (Howard-Varona et al., 2018).”
The Hologenome Concept: Human, Animal and Plant Microbiota (2014, background): “In addition to Bacteria, the human gut contains several species of Archaea and a large diversity of fungi (Hoffmann et al. 2013).”
Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease (2015, background): “Graphical abstract INTRODUCTION The human gut microbiota is densely populated by microbes from all three domains of life together with their viruses (Hoffmann et al., 2013; Human Microbiome Project, 2012; Samuel et al., 2007).”
Gut Microbiome: Profound Implications for Diet and Disease (2019, background): “In a mouse model, M. smithii has been shown to increase host adiposity by directing Bacteroides thetaiotaomicron to ferment plant polysaccharides (fructans) in the diet to the SCFA acetate [257].”
Human gut microbiota in health and disease: Unveiling the relationship (2022, background): “It is a prominent and essential Archean in the gut microbiota (Hoffmann et al., 2013; Berry, 2016).”