The colonization of the human gut microbiome begins at birth, and over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of microbial communities using genomic techniques, such as amplicon or shotgun metagenomic sequencing. Each method has distinct tradeoffs, but there has not been a direct comparison of the utility of these methods in stool samples from very young children, which have different features than those of adults. We compared the effects of profiling the human infant gut microbiome with 16S rRNA amplicon vs. shotgun metagenomic sequencing techniques in 338 fecal samples; younger than 15, 15–30, and older than 30 months of age. We demonstrate that observed changes in alpha-diversity and beta-diversity with age occur to similar extents using both profiling methods. We also show that 16S rRNA profiling identified a larger number of genera and we find several genera that are missed or underrepresented by each profiling method. We present the link between alpha diversity and shotgun metagenomic sequencing depth for children of different ages. These findings provide a guide for selecting an appropriate method and sequencing depth for the three studied age groups.
Oxygenic photosynthesis supplies organic carbon to the modern biosphere, but it is uncertain when this metabolism originated. Based on the inferred presence of manganese oxides in the sediments as old as 3 billion years, it has been proposed that photosynthetic reaction centers capable of splitting water arose by that time. However, this assumes that manganese oxides can only be produced in the presence of molecular oxygen 1 , reactive oxygen species 2,3 or by high-potential photosynthetic reaction centers 4,5 . Here we show that anoxygenic photosynthetic microbial communities biomineralize manganese oxides under strictly anaerobic conditions and in the absence of high-potential photosynthetic reaction centers. This light-dependent process can produce manganese oxide minerals and stimulate the redox cycling of carbon, sulfur, nitrogen and other elements in the photic zones of modern anoxic water bodies and sediments. Microbial oxidation of Mn(II) in the absence of molecular oxygen during the Archean Eon would have produced geochemical signals identical to those used to date the evolution of oxygenic photosynthesis before the Great Oxidation Event (GOE) 6,7 . Manganese (Mn) and more than 30 of its described oxides and hydroxides mediate the cycling of various trace metals and nutrients in the environment. The microbial ability to oxidize Mn(II) anaerobically is also hypothesized to have been a critical step in the evolution of oxygenic photosynthesis on the early Earth 4 . However, modern microbes are not known to anaerobically oxidize manganese. Here, we demonstrate this activity in active microbial cultures that grow in the presence of nanomolar oxygen concentrations relevant for the Archean Earth.Inoculum for the enrichment cultures of strictly anaerobic, photosynthetic biofilms came from the meromictic Fayetteville Green Lake (FGL), NY. The anaerobic photic zone of the lake contains 20 nM to 61 µM Mn(II) and 0-0.04 mM of H 2 S [8], and the most abundant phototroph there is the green sulfur bacterium Chlorobium sp. 9 . This microbe uses sulfide, hypothesized to be the oldest electron donor for photosynthesis 10 , as an electron donor. Photosynthetic biofilms of this organism and other strict anaerobes (Fig. 1a) were enriched in a minimal medium amended with 20-50 µM Na 2 S and 1 mM MnCl 2 and equilibrated with an anaerobic atmosphere of 80% N 2 and 20% CO 2 at pH 7. The concentration of O 2 in the medium was lower than 2 nM during the course of the experiment and the maximum total inflow of O 2 over two weeks was lower than 300 nmol (see Methods and Extended Data Fig. 1). These experimental concentrations match the upper estimates for the Archean Earth 11 . The anaerobic medium also lacked other potential oxidants for Mn(II) such as nitrite, nitrate and H 2 O 2 and these species were not produced in sterile controls (Extended Data Section 5). References 1 Tebo, B. M. et al. Biogenic manganese oxides: properties and mechanisms of formation.
The colonization of the human gut microbiome begins at birth, and, over time, these microbial communities become increasingly complex. Most of what we currently know about the human microbiome, especially in early stages of development, was described using culture-independent sequencing methods that allow us to identify the taxonomic composition of microbial communities using genomic techniques, such as amplicon or shotgun metagenomic sequencing. Each method has distinct tradeoffs, but there has not been a direct comparison of the utility of these methods in stool samples from very young children, which have different features than those of adults. We compared the effects of profiling the human infant gut microbiome with 16S rRNA amplicon versus shotgun metagenomic sequencing techniques in 130 fecal samples; younger than 15, 15-30, and older than 30 months of age. We demonstrate that observed changes in alpha-diversity and beta-diversity with age occur to similar extents using both profiling methods. We also show that 16S rRNA profiling identified a larger number of genera and we find several genera that are missed or underrepresented by each profiling method. We present the link between alpha diversity and shotgun metagenomic sequencing depth for children of different ages. These findings provide a guide for selecting an appropriate method and sequencing depth for the three studied age groups.
Bifidobacterium longum subsp. infantis (B. infantis) is one of a few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis. All three organisms are classified in the same species group but only B. infantis can metabolize human milk oligosaccharides (HMOs). We compared HMO-metabolizing genes across different Bifidobacterium genomes and developed B. infantis-specific primers to determine if the genes alone or the primers can be used to quickly characterize B. infantis. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, tested for its prevalence in infant gut metagenomes, and validated the results using the B. infantis-specific primers. We observed that only 15 of 203 (7.4%) children under 2 years old from a cohort of US children harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.
Both the brain and microbiome of humans develop rapidly in the first years of life, enabling extensive signaling between the gut and central nervous system (dubbed the “microbiome-gut-brain axis”). Emerging evidence implicates gut microorganisms and microbiota composition in cognitive outcomes and neurodevelopmental disorders (e.g., autism), but the influence of gut microbial metabolism on typical neurodevelopment has not been explored in detail. We investigated the relationship of the microbiome with the neuroanatomy and cognitive function of 281 healthy children in a cross-sectional analysis and demonstrated that differences in gut microbial taxa and gene functions are associated with the size of brain regions and with overall cognitive function. Many species, including Eubacterium eligens and Roseburia hominis, were associated with higher cognitive function, while some species such as Ruminococcus gnavus was more commonly found in children with low cognitive scores. Microbial enzymes involved in the metabolism of neuroactive compounds such as glutamate and GABA, were also associated with structure of the brain, including the first brain regions to develop such as the cerebellum, and with overall cognitive function.
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