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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Prosthetic joint infections present diverse and unique microbial communities using combined whole-genome shotgun sequencing and culturing methods
Introduction. Prosthetic joint infections (PJIs) are challenging to treat therapeutically because the infectious agents often are resistant to antibiotics and capable of abundant growth in surface-attached biofilms. Though infection rates are low, ca. 1–2 %, the overall increase in the sheer number of joint replacement surgeries results in an increase in patients at risk.
Aims. This study investigates the consensus of microbial species comprising PJI ecology, which is currently lacking.
Methodology. In this study, PJI populations from seven patients were analysed using combined culturing and whole-genome shotgun sequencing (WGSS) to establish population profiles and compare WGSS and culture methods for detection and identification of the PJI microbiome.
Results. WGSS detected strains when culture did not, notably dormant, culture-resistant and rare microbes. The CosmosID algorithm was used to predict micro-organisms present in the PJI and discriminate contaminants. However, culturing indicated the presence of microbes falling below the WGSS algorithm threshold. In these instances, microbes cultured are believed to be minor species. The two strategies were combined to build a population profile.
Conclusions. Variability between and among PJIs showed that most infections were distinct and unique. Comparative analysis of populations revealed PJIs to form clusters that were related to, but separate from, vaginal, skin and gut microbiomes. Fungi and protists were detected by WGSS, but the role of fungi is just beginning to be understood and for protists it is unknown. These micro-organisms and their novel and strain-specific microbial interactions remain to be determined in current clinical tests.
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Poo and Puns: The representation of Faecal Microbiota Transplants in English-language print media (2003 – 2017)
More LessThis study investigates how English-language news sources represented faecal microbiota transplants (FMT) between 2003 and 2017. In the context of this study, FMT is understood to be the process of transferring stool from a healthy donor to a recipient with a dysfunctional intestinal flora in order to repopulate their gut microbiome. A corpus of news articles on FMT, was produced by searching for ‘fa(e)cal microbial’, ‘microbiota transplant‘ and ‘stool transplant’ on the Nexis® UK news database, generating a corpus suitable for qualitative analysis (n = 504 articles). In order to uncover emerging social representations, we investigated press coverage of stool transplants, as well as broader themes associated with health and the gut microbiome. Our findings show that print media focused particularly on creating novel, mainly hopeful, social representations of faeces through wordplay and punning, side-lining issues of risk and fear. We also identify changing metaphorical framings of microbes and bacteria from ‘enemies’ to ‘friends’. Additionally, we found readers are familiarised with FMT through the depiction of the process as being both mundane and highly medicalised. We argue emerging media representations have the potential to shape more positive social representations of FMT in the general population, paving the way for FMT to become a more socially acceptable and effective medical procedure. Future research can build on this baseline in order to study how social representations circulate in the wider media and public sphere, and how they may change over time and differ between countries as research into FMT progresses.
https://www.tandfonline.com/doi/full/10.1080/14636778.2019.1637721
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Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes
Firmicutes and Bacteroidetes are the predominant bacterial phyla colonizing the healthy human large intestine. Whilst both ferment dietary fibre, genes responsible for this important activity have been analysed only in the Bacteroidetes, with very little known about the Firmicutes. This work investigates the carbohydrate-active enzymes (CAZymes) in a group of Firmicutes, Roseburia spp. and Eubacterium rectale, which play an important role in producing butyrate from dietary carbohydrates and in health maintenance. Genome sequences of 11 strains representing E. rectale and four Roseburia spp. were analysed for carbohydrate-active genes. Following assembly into a pan-genome, core, variable and unique genes were identified. The 1840 CAZyme genes identified in the pan-genome were assigned to 538 orthologous groups, of which only 26 were present in all strains, indicating considerable inter-strain variability. This analysis was used to categorize the 11 strains into four carbohydrate utilization ecotypes (CUEs), which were shown to correspond to utilization of different carbohydrates for growth. Many glycoside hydrolase genes were found linked to genes encoding oligosaccharide transporters and regulatory elements in the genomes of Roseburia spp. and E. rectale, forming distinct polysaccharide utilization loci (PULs). Whilst PULs are also a common feature in Bacteroidetes, key differences were noted in these Firmicutes, including the absence of close homologues of Bacteroides polysaccharide utilization genes, hence we refer to Gram-positive PULs (gpPULs). Most CAZyme genes in the Roseburia/E. rectale group are organized into gpPULs. Variation in gpPULs can explain the high degree of nutritional specialization at the species level within this group.
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Probiotics or antibiotics: future challenges in medicine
Genetic and environmental factors can affect the intestinal microbiome and microbial metabolome. Among these environmental factors, the consumption of antibiotics can significantly change the intestinal microbiome of individuals and consequently affect the corresponding metagenome. The term ‘probiotics’ is related to preventive medicine rather than therapeutic procedures and is, thus, considered the opposite of antibiotics. This review discusses the challenges between these opposing treatments in terms of the following points: (i) antibiotic resistance, the relationship between antibiotic consumption and microbiome diversity reduction, antibiotic effect on the metagenome, and disease associated with antibiotics; and (ii) probiotics as living drugs, probiotic effect on epigenetic alterations, and gut microbiome relevance to hygiene indulgence. The intestinal microbiome is more specific for individuals and may be affected by environmental alterations and the occurrence of diseases.
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