Human milk stimulates a health-promoting gut microbiome in infants. However, it is unclear how the microbiota salvages and processes its required nitrogen from breast milk. Human milk nitrogen sources such as urea could contribute to the composition of this early life microbiome. Urea is abundant in human milk, representing a large part of the non-protein nitrogen (NPN). We found that B. longum subsp. infantis (ATCC17930) can use urea as a main source of nitrogen for growth in synthetic medium and enzyme activity was induced by the presence of urea in the medium. We furthermore confirmed the expression of both urease protein subunits and accessory proteins of B. longum subsp. infantis through proteomics. To the same end, metagenome data were mined for urease-related genes. It was found that the breastfed infant's microbiome possessed more urease-related genes than formula fed infants (51.4:22.1; 2.3-fold increase). Bifidobacteria provided a total of 106 of urease subunit alpha alignments, found only in breastfed infants. These experiments show how an important gut commensal that colonizes the infant intestine can metabolise urea. The results presented herein further indicate how dietary nitrogen can determine bacterial metabolism in the neonate gut and shape the overall microbiome.

Marine photosynthetic microalgae are ubiquitously associated with bacteria in nature. However, the influence of these bacteria on algal cultures in bioreactors is still largely unknown. In this study, eighteen different bacterial strains were isolated from cultures of Nannochloropsis sp. CCAP211/78 in two outdoor pilot-scale tubular photobioreactors. The majority of isolates was affiliated with the classes Alphaproteobacteria and Flavobacteriia. To assess the impact of the eighteen strains on the growth of Nannochloropsis sp. CCAP211/78, 24-well plates coupled with custom-made LED boxes were used to simultaneously compare replicate axenic microalgal cultures with addition of individual bacterial isolates. Co-culturing of Nannochloropsis sp. CCAP211/78 with these strains demonstrated distinct responses, which shows that the technique we developed is an efficient method for screening the influence of harmful/beneficial bacteria. Two of the tested strains, namely a strain of Maritalea porphyrae (DMSP31) and a Labrenzia aggregata strain (YP26), significantly enhanced microalgal growth with a 14% and 12% increase of the chlorophyll concentration, respectively, whereas flavobacterial strain YP206 greatly inhibited the growth of the microalga with 28% reduction of the chlorophyll concentration. Our study suggests that algal production systems represent a 'natural' source to isolate and study microorganisms that can either benefit or harm algal cultures.

Evidence from cross-sectional human studies, and preliminary microbial-based intervention studies, have implicated the microbiota-gut-brain axis in the neurobiology of autism spectrum disorder (ASD). Using a prospective longitudinal study design, we investigated the developmental profile of the fecal microbiota and metabolome in infants with (n = 16) and without (n = 19) a family history of ASD across the first 36 months of life. In addition, the general developmental levels of infants were evaluated using the Mullen Scales of Early Learning (MSEL) test at 5 and 36 months of age, and with ADOS-2 at 36 months of age. At 5 months of age, infants at elevated-likelihood of ASD (EL) harbored less Bifidobacterium and more Clostridium and Klebsiella species compared to the low-likelihood infants (LL). Untargeted metabolic profiling highlighted that LL infants excreted a greater amount of fecal γ-aminobutyric acid (GABA) at 5 months, which progressively declined with age. Similar age-dependent patterns were not observed in the EL group, with GABA being consistently low across all timepoints. Integrated microbiome-metabolome analysis showed a positive correlation between GABA and Bifidobacterium species and negative associations with Clostridium species. In vitro experiments supported these observations demonstrating that bifidobacteria can produce GABA while clostridia can consume it. At the behavioral level, there were no significant differences between the EL and LL groups at 5 months. However, at 36 months of age, the EL group had significantly lower MSEL and ADOS-2 scores compared to the LL group. Taken together, the present results reveal early life alterations in gut microbiota composition and functionality in infants at elevated-likelihood of ASD. These changes occur before any behavioral impairments can be detected, supporting a possible role for the gut microbiota in emerging behavioral variability later in life.

The human gut ecosystem starts developing at birth and is influenced by many factors during early life. In this study we make use of a Belgian cohort of 64 children, followed until the age of 6 years, to analyze different phases of microbiota development. We analyzed fecal samples taken before weaning (age 1 month), shortly after weaning (age 6 months), when milk feeding has been discontinued completely (age 1 year), and at the age of 6 years. We performed 16S rRNA gene amplicon sequencing on the collected fecal samples and analyzed the compositional data in relation to dietary metadata and birth mode. Human and formula milk feeding promotes a microbiota dominated by either Bacteroides or Bifidobacterium, respectively. Into later life stages, the microbiota composition follows distinct microbiota clusters, related to abundance dynamics of certain bacterial groups. Furthermore, it becomes apparent that a formula diet leads to early maturation of the infant gut microbiota. Despite other clinical variables within the infant cohort, they did not significantly contribute to the microbiota patterns we observed. Our data provide a proof of principle study of the importance of diet to the development of the microbiota in early life that replicates earlier findings in other cohorts.

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