Unlocking the world of microbiomes
In 2020 we celebrate 75 years of the anniversary of our founding with a year of activities dedicated to demonstrating the impact of microbiologists’ past, present and future – bringing together and empowering communities that help shape the future of microbiology. We are launching new collections of digital content throughout the anniversary year. The first digital hub is Unlocking the world of microbiomes: exploring microbial communities, which will examine the microbiome and human health, agriculture and food microbiomes and environmental and industrial microbiomes.
The ‘Unlocking the world of microbiomes’ collection brings together articles from across our journals exploring microbial communities and examining the microbiome and human health. This collection is an update of a collection by the Microbiology Society and the British Society for Immunology launched for World Microbiome Day; the ‘Microbiome’ collection can be viewed on Science Open.
Collection Contents
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Sucrose 6F-phosphate phosphorylase: a novel insight in the human gut microbiome
The human gut microbiome plays an essential role in maintaining human health including in degradation of dietary fibres and carbohydrates further used as nutrients by both the host and the gut bacteria. Previously, we identified a polysaccharide utilization loci (PUL) involved in sucrose and raffinose family oligosaccharide (RFO) metabolism from one of the most common Firmicutes present in individuals, Ruminococcus gnavus E1. One of the enzymes encoded by this PUL was annotated as a putative sucrose phosphate phosphorylase (RgSPP). In the present study, we have in-depth characterized the heterologously expressed RgSPP as sucrose 6F-phosphate phosphorylase (SPP), expanding our knowledge of the glycoside hydrolase GH13_18 subfamily. Specifically, the enzymatic characterization showed a selective activity on sucrose 6F-phosphate (S6FP) acting both in phosphorolysis releasing alpha-d-glucose-1-phosphate (G1P) and alpha-d-fructose-6-phosphate (F6P), and in reverse phosphorolysis from G1P and F6P to S6FP. Interestingly, such a SPP activity had never been observed in gut bacteria before. In addition, a phylogenetic and synteny analysis showed a clustering and a strictly conserved PUL organization specific to gut bacteria. However, a wide prevalence and abundance study with a human metagenomic library showed a correlation between SPP activity and the geographical origin of the individuals and, thus, most likely linked to diet. Rgspp gene overexpression has been observed in mice fed with a high-fat diet suggesting, as observed for humans, that intestine lipid and carbohydrate microbial metabolisms are intertwined. Finally, based on the genomic environment analysis, in vitro and in vivo studies, results provide new insights into the gut microbiota catabolism of sucrose, RFOs and S6FP.
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Short- and long-term influence of the levonorgestrel-releasing intrauterine system (Mirena®) on vaginal microbiota and Candida
More LessBackground. Recurrent vulvovaginal infections are a frequent complaint in young women in need of contraception. However, the influence of the contraceptive method on the course of the disease is not well known.
Aim. To investigate the influence of the levonorgestrel-releasing intrauterine-system (LNG-IUS) on the vaginal microflora.
Methods. Short-term (3 months) and long-term (1 to 5 years) changes of vaginal microbiota were compared with pre-insertion values in 252 women presenting for LNG-IUS insertion. Detailed microscopy on vaginal fluid was used to define lactobacillary grades (LBGs), bacterial vaginosis (BV), aerobic vaginitis (AV) and the presence of Candida. Cultures for enteric aerobic bacteria and Candida were used to back up the microscopy findings. Fisher's test was used to compare vaginal microbiome changes pre- and post-insertion.
Results. Compared to the pre-insertion period, we found a temporary worsening in LBGs and increased rates of BV and AV after 3 months of LNG-IUS. After 1 and 5 years, however, these changes were reversed, with a complete restoration to pre-insertion levels. Candida increased significantly after long-term carriage of LNG-IUS compared to the period before insertion [OR 2.0 (CL951.1–3.5), P=0.017].
Conclusions. Short-term use of LNG-IUS temporarily decreases lactobacillary dominance, and increases LBG, AV and BV, but after 1 to 5 years these characteristics return to pre-insertion levels, reducing the risk of complications to baseline levels. Candida colonization, on the other hand, is twice as high after 1 to 5 years of LNG-IUS use, making it less indicated for long-term use in patients with or at risk for recurrent vulvovaginal candidosis.
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Sequence-based analysis of the genus Ruminococcus resolves its phylogeny and reveals strong host association
More LessIt has become increasingly clear that the composition of mammalian gut microbial communities is substantially diet driven. These microbiota form intricate mutualisms with their hosts, which have profound implications on overall health. For example, many gut microbes are involved in the conversion of host-ingested dietary polysaccharides into host-usable nutrients. One group of important gut microbial symbionts are bacteria in the genus Ruminococcus. Originally isolated from the bovine rumen, ruminococci have been found in numerous mammalian hosts, including other ruminants, and non-ruminants such as horses, pigs and humans. All ruminococci require fermentable carbohydrates for growth, and their substrate preferences appear to be based on the diet of their particular host. Most ruminococci that have been studied are those capable of degrading cellulose, much less is known about non-cellulolytic non-ruminant-associated species, and even less is known about the environmental distribution of ruminococci as a whole. Here, we capitalized on the wealth of publicly available 16S rRNA gene sequences, genomes and large-scale microbiota studies to both resolve the phylogenetic placement of described species in the genus Ruminococcus, and further demonstrate that this genus has largely unexplored diversity and a staggering host distribution. We present evidence that ruminococci are predominantly associated with herbivores and omnivores, and our data supports the hypothesis that very few ruminococci are found consistently in non-host-associated environments. This study not only helps to resolve the phylogeny of this important genus, but also provides a framework for understanding its distribution in natural systems.
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The soil microbiome at the Gi-FACE experiment responds to a moisture gradient but not to CO2 enrichment
More LessThe soil bacterial community at the Giessen free-air CO2 enrichment (Gi-FACE) experiment was analysed by tag sequencing of the 16S rRNA gene. No substantial effects of CO2 levels on bacterial community composition were detected. However, the soil moisture gradient at Gi-FACE had a significant effect on bacterial community composition. Different groups within the Acidobacteria and Verrucomicrobia phyla were affected differently by soil moisture content. These results suggest that modest increases in atmospheric CO2 may cause only minor changes in soil bacterial community composition and indicate that the functional responses of the soil community to CO2 enrichment previously reported at Gi-FACE are due to factors other than changes in bacterial community composition. The effects of the moisture gradient revealed new information about the relationships between poorly known Acidobacteria and Verrucomicrobia and soil moisture content. This study contrasts with the relatively small number of other temperate grassland free-air CO2 enrichment microbiome studies in the use of moderate CO2 enrichment and the resulting minor changes in the soil microbiome. Thus, it will facilitate the development of further climate change mitigation studies. In addition, the moisture gradient found at Gi-FACE contributes new knowledge in soil microbial ecology, particularly regarding the abundance and moisture relationships of the soil Verrucomicrobia.
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