Unlocking the world of microbiomes

A Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterium, named strain LZ-16-2T, was isolated from the phycosphere microbiota of the paralytic shellfish poisoning toxin-producing marine dinoflagellate Alexandrium catenella LZT09. Strain LZ-16-2T grew optimally at 28 °C at pH 6.5 and with 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain LZ-16-2T fell within the genus Haliea and was most closely related to Haliea salexigens DSM 19537T, with which the new isolate exhibited 98.5 % 16S rRNA gene sequence similarity. The major respiratory quinone was Q-8. The predominant cellular fatty acids were C17 : 1  ω8c, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C17 : 1  ω6c, C11 : 0 3-OH and C17 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The average nucleotide identity and in silico DNA–DNA genome hybridization relatedness values between strain LZ-16-2T and its closest relative, H. salexigens DSM 19537T, were 92.8 and 55.1 %, respectively. The DNA G+C content was 61.3 mol%. Differential phenotypic properties and phylogenetic distinctiveness distinguished strain LZ-16-2T from all other members of the genus Haliea . On the basis of the polyphasic characterization, strain LZ-16-2T represents a novel species of the genus Haliea , for which the name Haliea alexandrii sp. nov. is proposed. The type strain is LZ-16-2T (=KCTC 62344T=CCTCC AB2017229T).

Neuropsychiatric disorders (NPDs) such as depression, anxiety, bipolar disorder, autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD) all relate to behavioural, cognitive and emotional disturbances that are ultimately rooted in disordered brain function. More specifically, these disorders are linked to various neuromodulators (i.e. serotonin and dopamine), as well as dysfunction in both cognitive and socio-affective brain networks. Increasing evidence suggests that the gut environment, and particularly the microbiome, plays a significant role in individual mental health. Although the presence of a gut–brain communication axis has long been established, recent studies argue that the development and regulation of this axis is dictated by the gut microbiome. Many studies involving both animals and humans have connected the gut microbiome with depression, anxiety and ASD. Microbiome-centred treatments for individuals with these same NPDs have yielded promising results. Despite its recent rise and underlying similarities to other NPDs, both biochemically and symptomatically, connections between the gut microbiome and ADHD currently lag behind those for other NPDs. We demonstrate that all evidence points to the importance of, and dire need for, a comprehensive and in-depth analysis of the role of the gut microbiome in ADHD, to deepen our understanding of a condition that affects millions of individuals worldwide.

The human gut is populated with a vast community of microbes, the microbiota. Fungi comprise 0.1% of the total gut microbiota. Some of these fungi exist as benign members, however others such Candida albicans can undergo a pathogenic switch causing disease. The fungal cell wall is the first target for immune system recognition. Recent studies have suggested that Candida is decorated with different cell wall epitopes within different physiological niches, due to the impact of carbon source and oxygen availability on cell wall remodelling. Here we hypothesize that resident gut bacteria also play a major role in fungal cell wall remodelling and immune recognition. Data from our lab has shown that a common bacterium from the gut, Bacteroides thetaiotaomicron (Bt), produces an extensive repertoire of degradative enzymes to breakdown the Candida cell wall. Recently, we have identified novel enzymes in Bt from the glycoside hydrolase family 130 (GH130), which specifically target β1,2-linked mannan, a unique feature of Candida mannan. We have deleted multiple fungal mannan specific loci in Bt and examined the ability of deletion strains to utilise Candida mannan as a carbon source. These data suggest that Bt contains multiple pathways to degrade the Candida cell wall. Now we are systematically dissecting the impact of mannan degradation on the physiology of the fungus. This will provide insights into how two prominent members of the gut microbiota interact with each other, how the Candida cell wall is modified in the anaerobic environment of the gut, and the importance of this in promoting immune homeostasis.

Automated, high-throughput technologies are becoming increasingly common in microbiome studies to decrease costs and increase efficiency. However, in microbiome studies, small differences in methodology – including storage conditions, wet lab methods, sequencing platforms and data analysis – can influence the reproducibility and comparability of data across studies. There has been limited testing of the effects of high-throughput methods, including microfluidic PCR technologies. In this paper, we compare two extraction methods (the QIAamp DNA Stool Mini Kit and the MoBio PowerSoil DNA Isolation kit), two taq polymerase enzymes (MyTaq HS Red Mix and Accustart II PCR ToughMix), two primer sets (V3–V4 and V4–V5) and two amplification methods (a common two-step PCR protocol and amplicon library preparation on the Fluidigm Access Array system that allows automated multiplexing of primers). Gut microbial community profiles were significantly affected by all variables. While there were no significant differences in alpha diversity measured between the two extraction methods, there was an effect of extraction method on community composition measured by unweighted UniFrac distances. Both amplification method and primers had a significant effect on both alpha diversity and community composition. The relative abundance of Actinobacteria was significantly lower when using the MoBio kit or Fluidigm amplification method, and the relative abundance of Firmicutes was lower when using the Qiagen kit. Microbial community profiles based on Fluidigm-generated amplicon libraries were not comparable to those generated with more commonly used methods. Researchers should carefully consider the limitations and biases that different extraction and amplification methods can introduce into their results. Additionally, more thorough benchmarking of automated and multiplexing methods is necessary to determine the magnitude of the potential trade-off between the quality and the quantity of data.

Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson’s index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium . In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii . In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.

This 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

Enterococcus faecium is a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing-based study on 96 multidrug-resistant E. faecium strains that asymptomatically colonized five patients with the aim of describing the genome dynamics of this species. The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged to E. faecium clade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which consisted entirely of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalization. We estimated the evolutionary rate of two clonal groups that each colonized single patients at 12.6 and 25.2 single-nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of 12 different insertion sequence (IS) elements, with ISEfa5 showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5 excision and insertion into the genome during gut colonization. Our findings show that the E. faecium genome is highly dynamic during asymptomatic colonization of the human gut. We observed considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.

The casing material required in mushroom cultivation presents a very rich ecological niche, which is inhabited by a diverse population of bacteria and fungi. In this work three different casing materials, blonde peat, black peat and a 50 : 50 mixture of both, were compared for their capacity to show a natural suppressive response against dry bubble, Lecanicillium fungicola (Preuss) Zare and Gams, and wet bubble, Mycogone perniciosa (Magnus) Delacroix. The highest mushroom production was collected from crops cultivated using the mixed casing and black peat, which were not significantly different in yield. However, artificial infection with mycoparasites resulted in similar yield losses irrespective of the material used, indicating that the casing materials do not confer advantages in disease suppression. The composition of the microbiome of the 50 : 50 casing mixture along the crop cycle and the compost and basidiomes was evaluated through next-generation sequencing (NGS) of the V3–V4 region of the bacterial 16S rRNA gene and the fungal ITS2 region. Once colonized by Agaricus bisporus, the bacterial diversity of the casing microbiome increased and the fungal diversity drastically decreased. From then on, the composition of the casing microbiome remained relatively stable. Analysis of the composition of the bacterial microbiome in basidiomes indicated that it is highly influenced by the casing microbiota. Notably, L. fungicola was consistently detected in uninoculated control samples of compost and casing using NGS, even in asymptomatic crops. This suggests that the naturally established casing microbiota was able to help to suppress disease development when inoculum levels were low, but was not effective in suppressing high pressure from artificially introduced fungal inoculum. Determination of the composition of the casing microbiome paves the way for the development of synthetic casing communities that can be used to investigate the role of specific components of the casing microbiota in mushroom production and disease control.

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.

Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites.