Microbiome & Nutrition

Nature Microbiology and Nature Communications are issuing a joint call for papers to highlight research focused on microbiome and nutrition.

In this review article, the authors provide an overview of the interrelationships between the microbiome and nutrition in child growth and healthy development and discuss the potential of the microbiome in undernutrition interventions.

Microbiota-targeted interventions for malnutrition are under investigation, but complex illnesses associated with malnutrition, such as eating disorders, may not be straightforward to treat.

Dysbiosis of the gut microbiome confers alterations in appetitive and metabolic regulation of body weight in anorexia nervosa in humans and mice.

In this Review article, the authors discuss the potential of microorganisms as a solution to the challenges faced by our food system. Engineered microorganisms can be used to produce enhanced foods and ingredients in a sustainable manner. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.

Tracking the journey of inulin, a soluble dietary fibre, reveals its fate and transformation by the gut microbiota to alleviate liver disease in mice.

Dietary fibre deprivation in mice increases the abundance of gut microbial mucin-degrading species, leads to barrier dysfunction and increases local type 2 inflammation. In a tractable human microbiota mouse model, the presence of Akkermansia muciniphila results in increased anti-commensal IgE and type 2 immune responses, worsening food allergy symptoms following sensitization.

Lactulose is used to treat patients with hepatic encephalopathy but this prebiotic can also increase intestinal Bifidobacteria, thereby reducing systemic infection, growth of multidrug-resistant bacteria and mortality that often accompanies chronic liver disease.

A ‘reverse translation’ strategy using gnotobiotic mice ascertains cause and effect relationships between bacterial members of the gut microbiota, dietary components and host physiology, which are difficult to establish in human nutritional trials.

A postnatal multiple micronutrient deficiency mouse model reveals shifts in bacterial, fungal and viral components of the gut microbiome with implications for microbiome-encoded intrinsic antibiotic resistance mechanisms.

Prevotella copri, together with other microbiota members, plays a key role in mediating the beneficial effects of a gut microbiota-directed complementary food for malnourished children on microbiota and host functions.

Here, combining metabolomic, proteomic and biophysical analyses, the authors identify and characterize a series of diindole molecules produced from commensal bacteria metabolites that act as specific agonists for the orphan constitutive androstane receptor (CAR), having potential to modulate gut and liver inflammation, metabolic diseases and cancer.

Here, Zhang et al. identify a metabolic axis by which Lys-producing commensal bacterium Dubosiella newyorkensis mediates a Treg-mediated immunosuppressive microenvironment by activating AhR-IDO1-Kyn metabolic circuitry in dendritic cells.

Here, the authors present the results of the PROMOTe trial, reporting improved cognition with prebiotic vs placebo in twins over 60 years old, probing that remote trials are feasible in older adults, and suggesting that the gut microbiota may represent a therapeutic target for age-associated morbidity.

Here, the authors present a comparative analysis of the diet, microbiome and metabolome of rural and urban Xhosa people in South Africa, associating urban diets with higher abundances of pro-neoplastic microbial metabolites.

Here, the authors develop a high-throughput method to quantify Bifidobacterium longum subsp. infantis (BL. infantis), a proficient HMO-utilizer, from metagenomic sequencing, and applied it to a longitudinal cohort consisting of 21 mother-infant dyads, suggesting BL. infantis colonization to start late in the breast-feeding period.

Here, Lou et al. apply metagenomics and microbiome cultivation to infant fecal samples and uncover co-existing members encoding extracellular fucosidases that initiate 2’-fucosyllactose (2’FL) breakdown and can promote extensive growth of Bifidobacterium breve.

Here, Schoeler et al. investigate how interaction between dietary lipids and the gut microbiota affect hepatic steatosis and host metabolism, showing that dietary lipids impact the gut microbiota composition independent on fiber intake in humans and mice.

Here, analyzing data from a six-month clinical trial in pre-diabetes, the authors found 166 of 2,803 measured features, including oral and gut microbiome, metabolites and cytokines, significantly changed in response to dietary interventions; highlighting the microbiome’s role in cardiometabolic health and revealing potential therapeutic avenues.

The gut commensal Christensenalla minuta produces a previously undescribed class of secondary bile acids that counteract features of metabolic disease and are depleted in patients with type 2 diabetes.

Characterization of quorum sensing-regulated antibiotic production by Streptococcus salivarus and signal eavesdropping by Streptococcus pyogenes enables engineering of a probiotic strain to prevent pathogen signal eavesdropping and antibiotic degradation, and inhibit colonization.

Three distinct families of gut bacteria encode an unprecedented number of respiratory-like reductases per genome to perform anaerobic respiration of biomedically relevant substrates.

A multi-omics approach reveals that bifidobacteria metabolize the prebiotic lactulose to produce acetate and deconjugate bile acids, which is associated with reduced densities of drug-resistant pathogens and decreased incidences of infection in patients with liver disease.

The gut commensal Akkermansia muciniphila regulates food allergy symptoms in a diet-dependent manner in mice.

The gut commensal Parabacteroides distasonis uses inulin to produce the odd-chain fatty acid pentadecanoic acid, which alleviates non-alcoholic steatohepatitis via improved barrier function in mice.

Faecal metagenomics and serum metabolomics reveal compositional and functional alterations in the gut microbiota of women with anorexia nervosa, and faecal transplants could transfer an anorexia-associated phenotype to germ-free mice.

Different populations of Campylobacteraceae co-exist in the cow rumen epithelial microbiome thanks to metabolic trade-offs in utilization of versus inhibition by acetate and propionate, with implications for host carbon uptake.

Metagenomics and metabolomics analysis of a longitudinal cohort of 123 very preterm infants reveals multiple drivers of gut microbiome development and indicates that there are strain-specific effects of probiotic products.

Here, using metagenomics, the authors show that the gut microbiome of rural Zimbabwean infants undergoes programmed maturation that is unresponsive to sanitation and nutrition interventions but is strongly associated with maternal HIV infection and can moderately predict linear growth.

Interplay of western diet and gut microbiota has been reported to be involved in the development of nonalcoholic steatohepatitis (NASH). Here the authors report that Blautia producta and 2-oleoylglycerol are bacterial and metabolic mediators that promote liver inflammation and hepatic fibrosis in male mice.

In this study, 591 mice from an advanced-intercross mouse line were used to provide evidence that fungi are regulated by host genetics, while uncovering a regulatory role of diet on the composition of fungi in the murine gut.

Giardia lamblia intestinal infection is independently associated with faltering linear growth in children in low-middle income countries, yet the mechanistic pathway has not been clearly identified. Authors utilise the MAL-ED cohort, and a gnotobiotic murine model, to explain Giardia-induced effects on childhood growth.

Choi, Jung and Lee highlight ways to produce renewable microbial foods that could move us closer to carbon neutrality.