Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection

Understanding how exogenous microbes stably colonize the animal gut is essential to reveal mechanisms of action and tailor effective probiotic treatments. Bifidobacterium species are naturally enriched in the gastrointestinal tract of breast-fed infants. Human milk oligosaccharides (HMOs) are associated with this enrichment. However, direct mechanistic proof of the importance of HMOs in this colonization is lacking given milk contains additional factors that impact the gut microbiota. This study examined mice supplemented with the HMO 2'fucosyllactose (2'FL) together with a 2'FL-consuming strain, Bifidobacterium pseudocatenulatum MP80. 2'FL supplementation creates a niche for high levels of B.p. MP80 persistence, similar to Bifidobacterium levels seen in breast-fed infants. This synergism impacted gut microbiota composition, activated anti-inflammatory pathways and protected against chemically-induced colitis. These results demonstrate that bacterial-milk glycan interactions alone drive enrichment of beneficial Bifidobacterium and provide a model for tunable colonization thus facilitating insight into mechanisms of health promotion by bifidobacteriain neonates.

The fecal resistome of dairy cattle is associated with diet during nursing

Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly

The factors that govern assembly of the gut microbiota are insufficiently understood. Here, we test the hypothesis that inter-individual microbiota variation can arise solely from differences in the order and timing by which the gut is colonized early in life. Experiments in which mice were inoculated in sequence either with two complex seed communities or a cocktail of four bacterial strains and a seed community revealed that colonization order influenced both the outcome of community assembly and the ecological success of individual colonizers. Historical contingency and priority effects also occurred in Rag1^-/- mice, suggesting that the adaptive immune system is not a major contributor to these processes. In conclusion, this study established a measurable effect of colonization history on gut microbiota assembly in a model in which host and environmental factors were strictly controlled, illuminating a potential cause for the high levels of unexplained individuality in host-associated microbial communities.

The microbial community living in the gastrointestinal tract of humans, also known as the gut microbiome, is essential for health. Disturbances of this community can lead to chronic diseases. Each person has a unique and stable community of gut microbes that is as personal as a ‘fingerprint’. Studies have shown that an individual’s genetics, diet, environment, lifestyle, and physiological state all make small contributions to the variation of the gut microbiome among individuals. However, less than 30% of this variation can be explained, and even identical twins, who share the same genetics and often diets and lifestyle, have distinct gut microbiomes. This suggests that other unknown factors likely shape these microbial communities too.

The microbial communities and the gut make up an ecosystem that is likely subject to many of the same ecological rules that govern ecosystems like rainforests or coral reefs. Yet many studies have overlooked the role of ecology in shaping the gut microbiota. For example, it is well known that the order in which organisms arrive in a community may influence how they interact and assemble into communities. It is possible that the order bacteria are introduced into the gastrointestinal tract of babies early in life may also change the make up of their gut microbiome, and thus introduce the variation that is currently unaccounted for.

Now, Martínez et al. show that the first types of bacteria to colonize the gut of mice have a lasting impact on their microbiome. In the experiments, genetically identical mice were housed under exactly the same conditions in airtight plastic bubbles. This allowed the scientists to control when the young mice first encountered specific microbes and microbe communities. Distinct microbial communities collected from different adult mice were introduced into the gastrointestinal tract of the young mice in sequence. Martínez et al. found that the microbes they introduced into the young mice first had the strongest influence on their gut microbiome at the end of the experiments.

When the experiments were repeated with a cocktail of four different bacteria the results were similar – the earlier arrivals showed enhanced colonization and had the biggest influence on the microbe community. This suggests that the timing of bacterial arrival in the gut is very important to shape the gut microbiome. Since it is highly random and unpredictable in real-life, and likely to differ even among twins, it could explain why the gut microbiome can be so unique. More studies are needed to understand how antibiotics, formula feeding, or cesarean sections affect gut microbiota early in life, and consequently health. This may help scientists develop better ways to influence the microbiota to improve health, for example, by introducing beneficial microbes early in life.