Unusual, large, and alternatively coded phages are prevalent in the human microbiome
Prof Jillian Banfield
Rare transmission of commensal and pathogenic bacteria in the gut microbiome of hospitalized adults
Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome
Background: Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 meters below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown, especially identifying the genetic mobility of resistance and pathogenicity in unculturable trench bacteria is a great challenge. This study aims to depict the landscape of virulome, antibiotic resistome and mobilome of the hadal zone microbiota of the Mariana Trench.
Method: The landscape of virulence and antibiotic resistance genes was depicted based on high-throughput metagenomic sequencing analysis using both sequence-based and domain-based annotation methods. The mobility and spread potentials of ARGs and virulence genes via horizontal gene transfer (HGT) were examined by checking their co-occurrence with MGEs.
Results and Discussion: i) the Challenger Deep bottom (10,898-m) sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance (Fig. 1b and 2b), compared with the other Marian Trench sediment; ii) both the abundance and richness of ARGs greatly differed across sediment sites in the following increasing trend: SM10898 < SM6038 < SP5856 (Fig. 2a). Surprisingly, the bottom site of the Challenger Deep was found to still harbor 20 subtypes of known ARGs. Both the abundance (1.08 to 1.12×10-1 GP16S each) and diversity (127 to 153 subtypes) of the hadal seawater ARGs (Fig. 2b) were surprisingly high in the hadal seawater of the Mariana trench. The abundance of ARGs in seawater is higher than that in sediments by up to two orders of magnitude, deterministic natural processes drivers the resistome differences between hadal sediment and seawater including habitat (environmental) filtering and biotic interactions (e.g., competition). iii) HGT mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria (Fig. 3a); iv) substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria (Fig. 4).
Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)
High-throughput sequencing is commonly used to study microorganisms in the environment without a need for culturing. Computational analysis of metagenomic has enabled the construction of large compendia of metagenome-assembled genomes (MAGs) from human-, animal-associated and environmental samples. Metagenomic binning is the step in the standard pipeline which groups the contigs into bins such that each bin is predicted to contain only contigs from the same genome.
Binning methods can be divided into reference-dependent (based on reference genomes) and reference-independent methods (operating de novo). Compared to reference-dependent methods, reference-independent methods can discover new species or even new phyla, but completely ignore any background information. To combine the advantages of these two categories, we propose a novel binning method called SemiBin which uses a semi-supervised neural network to incorporate information from reference genomes, while still being capable of finding novel species. SemiBin outperforms existing state-of-the-art binning methods in simulated and real microbiome datasets across three different environments (human gut, dog gut, and marine environments). SemiBin returns more high-quality bins (48.0-99.2% more in single-sample mode; 11.0-30.7% more in multi-sample mode, compared to the second-best alternative). Compared to the alternatives, SemiBin captures a larger taxonomic diversity, including more distinct genera and species. In particular, we verified that SemiBin can retrieve more genomes from both known and novel species.
SemiBin is available as open source software at https://github.com/BigDataBiology/SemiBin/.
Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
Impact of gut decontamination on the intestinal microbiome composition and the risk of bloodstream infection (BSI) in pediatric allogeneic hematopoietic stem cell transplant (allo-HSCT) patients
Gut decontamination (GD) is the practice of using non-absorbable antibiotics to alter the microbial composition in the digestive tract. Despite promising evidence in early studies indicating that GD may be protective against acute graft-versus-host-disease (aGVHD), there have been no definitive human studies showing that GD is beneficial for lowering the risk of aGVHD.
We present the results of the first randomized (1-to-1) phase 2 trial in pediatric allogeneic hematopoietic stem cell transplantation (allo-HSCT) investigating the effects of oral GD on the diversity of the gut microbiota (ClinicalTrials.gov Identifier: NCT02641236). 20 patients were enrolled and randomized to the intervention group (GD with oral vancomycin and polymyxin B from day -5 through neutrophil engraftment) or to the control group (no GD).
We demonstrate that between the GD and control arms, there is no statistical difference in Shannon diversity at 2 weeks post-transplant. Secondary analysis reveals no statistically significant difference in diarrhea at 7 days, acute GVHD by day +100, nor difference in antibiotic exposure during the first 30 days. While not statistically significant, we observed more bloodstream infections (BSI) (n = 5 vs. 1) in controls vs. those treated with GD. We thus postulated that GD may be decreasing the abundance of bloodstream infection-causing bacteria from the gut microbiome. By comparing the DNA sequences of the bacteremia causing bacteria and the stool samples from patients who developed these bacteremias, we found that both mucosal barrier injury-associated and non-mucosal barrier injury-associated pathogens can be found in the gut microbiome of HSCT patients. We thus postulate that GD may thus have an impact on decreasing the rate of BSIs, although this will need to be independently investigated in future, appropriately powered and designed studies. Taken together, in this small, phase 2 randomized control trial (RCT), we observed no difference in aGVHD incidence and overall survival in the two arms, but do observe a potential trend toward GD protecting from post-HSCT BSIs.
The gut microbiota in anxiety and depression - A systematic review
Growing evidence indicates the community of microorganisms throughout the gastrointestinal tract, (i.e., gut microbiota), is associated with anxiety and depressive disorders. We present the first systematic review of the gut microbiota in anxiety disorders, along with an update in depression. Consideration of shared underlying features is essential due to the high rates of comorbidity. Systematic searches, following PRISMA guidelines, identified 26 studies (two case-control comparisons of the gut microbiota in generalised anxiety disorder, 17 in depression, one incorporating both anxiety/depression, and five including symptom-only measures). Alpha and beta diversity findings were inconsistent; however, differences in bacterial taxa indicated disorders may be characterised by a higher abundance of proinflammatory species (e.g., Enterobacteriaceae and Desulfovibrio), and lower short-chain fatty acid producing-bacteria (e.g., Faecalibacterium). Several taxa, and their mechanisms of action, may relate to anxiety and depression pathophysiology via communication of peripheral inflammation to the brain. Although the gut microbiota remains a promising target for prevention and therapy, future research should assess confounders, particularly diet and psychotropic medications, and should examine microorganism function.
The composition of the oral resistome is altered by the presence of caries
Caries is the most prevalent global disease. Taxonomical studies to date suggest that changes in microbial membership may not fully explain dysbiosis. Therefore, functional characterisation of the plaque biofilm including its antimicrobial resistance (AMR) potential is required. The oral resistome is an inherent feature of the microbiome, yet its role in health and caries is poorly understood. More specifically, the oral resistome has the potential to influence the development of new dental materials which incorporate bioactive particles to modulate the caries microbiome. While these materials seek to improve oral health outcomes through minimal intervention, these particles must not create resistance. Our cross-sectional study aimed to describe the oral resistome by identifying and quantifying its membership in health and caries by analysing 58 metagenomes from 24 caries free and 34 caries affected children (mean age 8.8 + 1.38 years). 16S rRNA gene sequencing was also performed to assess bacterial diversity. No significant differences were found between the caries free and affected resistomes in terms of overall abundance and alpha diversity. However, the resistome at an antimicrobial gene (ARG) level had distinct profiles based on caries presence/absence and the depth of carious lesions. Differential abundance analyses revealed that five ARGs (aph 3’-Ib, aph 3”-IIIa, catA16, tet(A), tet(B)) were key drivers in the caries affected resistome. The caries free resistome covered a more diverse range of antibiotic classes and was potentially associated with more bacterial hosts than the caries affected resistome. Streptococcus mitis was commonly identified as a potential bacterial host in both groups. Functional analysis of insertion sequences and metabolic pathways associated with resistance found there were no significant differences between the caries free and affected groups. Environmental factors that modify caries risk were also investigated, including socio-economic status (access to dental care), asthma medications (corticosteroids and bronchodilators, that reduce salivary flow) and antibiotic exposure within the past 12 months. The only significant environmental association was the increased presence of the macrolide/lincosamide gene RlmA(II) in the low socio-economic status group. Our findings indicate that important associations may exist between the structure of the resistome in caries and health.
Maternal Immune Activation and the Gut Microbiome in Offspring
Introduction: Maternal immune activation (MIA), or the triggering of the maternal immune system during pregnancy, is a well-known risk factor for autism. Pre-clinical studies have suggested that MIA affects the gut microbiome composition of the offspring. Clinical studies of children with autism have also found gut microbiome differences between children with and without a diagnosis, although the evidence is conflicting, and the largest published studies report negligible association. The aim of our study was to fill the gap in the literature and assess the gut microbiome of children born to mothers with and without MIA.
Methods: This was a cross-sectional study which included children diagnosed with autism, siblings without a diagnosis and unrelated children without a diagnosis who were recruited into the Australian Autism Biobank. Data was analysed for 174 children, of whom 63 were born to mothers with MIA and 111 were born to mothers without MIA. MIA included asthma/allergies, complications during pregnancy, auto-immune conditions, and acute inflammation. Gut microbiome data was collected using shotgun metagenomic sequencing of child faecal samples. Results: Children born to mothers with MIA were more likely to be diagnosed with autism in this cohort. There was no significant difference between bacterial richness, α-diversity or β-diversity between groups. After adjusting for age, sex, diet, maternal stress and autism diagnosis, we still found no microbiome differences between the two groups. A single species, Faecalicatena torques, was found to be significantly increased in the MIA group in differential abundance analyses.
Discussion: To our knowledge, this is the first study to investigate the effect of MIA on the gut microbiome in children. Consistent with previous findings, we found that children who were born to mothers with MIA were more likely to be diagnosed with autism. Unlike pre-clinical studies, we found negligible microbiome differences between the MIA groups. Given the current interest in the microbiome-gut-brain axis, researchers should exercise caution in translating microbiome findings from pre-clinical models to a clinical setting. Microbiome-focused therapies for children with autism should be used with caution and need to be investigated further in relation to autism-related risk factors.
OPEN-ACCESS PAPER HIGHLIGHT
Commensal Microbiota Regulates Skin Barrier Function And Repair Via Signaling Through The Aryl Hydrocarbon Receptor
Commensal microbes are critical in maintaining skin homeostasis. However, their mechanisms of crosstalk with host epithelia remain poorly defined, especially during barrier disruption and repair. The goal of this study is to understand mechanisms by which skin microbiome impact barrier repair. Using germ free (GF) mice, we demonstrate that microbiota is necessary for proper differentiation and repair of the epidermal barrier. RNAseq was used to compare epithelial transcriptomes of GF mice to specific pathogen free (SPF) mice to identify microbially-regulated genetic pathways. Epithelial development and differentiation genes were downregulated in GF mice. Electron microscopy and immunofluorescence-based analyses revealed that GF mice have abnormal epidermal ultrastructure. GF mice were deficient in barrier repair compared to SPF mice following tape-stripping, as measured by transepidermal water loss (p<0.0001). A similar effect was observed after antibiotic depletion of microbiota in SPF mice. We identified the aryl hydrocarbon receptor (AhR) pathway as downregulated in GF epidermis (p=0.0033). Since AHR is a known regulator of epidermal differentiation, we hypothesized that skin microbiota engages in crosstalk with keratinocytes via the AhR to promote barrier repair. Murine skin lacking keratinocyte AHR was more susceptible to barrier damage and infection, during steady state and epicutaneous sensitization. Colonization with a defined consortium of human skin isolates restored barrier competence in an AHR-dependent manner. We reveal a fundamental mechanism whereby the microbiota regulates skin barrier formation and repair, with far-reaching implications for the numerous skin disorders characterized by epidermal barrier dysfunction.
Powerful and robust non-parametric association testing for microbiome data via a zero-inflated quantile approach (ZINQ)
Identification of bacterial taxa associated with diseases, exposures, and other variables of interest offers a more comprehensive understanding of the role of microbes in many conditions. However, despite considerable research in statistical methods for association testing with microbiome data, approaches that are generally applicable remain elusive. Classical tests often do not accommodate the realities of microbiome data, leading to power loss. Approaches tailored for microbiome data depend highly upon the normalization strategies used to handle differential read depth and other data characteristics, and they often have unacceptably high false positive rates, generally due to unsatisfied distributional assumptions. On the other hand, many non-parametric tests suffer from loss of power and may also present difficulties in adjusting for potential covariates. Most extant approaches also fail in the presence of heterogeneous effects. The field needs new non-parametric approaches that are tailored to microbiome data, robust to distributional assumptions, and powerful under heterogeneous effects, while permitting adjustment for covariates. As an alternative to existing approaches, we propose a zero-inflated quantile approach (ZINQ), which uses a two-part quantile regression model to accommodate the zero inflation in microbiome data. For a given taxon, ZINQ consists of a valid test in logistic regression to model the zero counts, followed by a series of quantile rank-score based tests on multiple quantiles of the non-zero part with adjustment for the zero inflation. As a regression and quantile-based approach, the method is non-parametric and robust to irregular distributions, while providing an allowance for covariate adjustment. Since no distributional assumptions are made, ZINQ can be applied to data that has been processed under any normalization strategy. Thorough simulations based on real data across a range of scenarios and application to real data sets show that ZINQ often has equivalent or higher power compared to existing tests even as it offers better control of false positives. We present ZINQ, a quantile-based association test between microbiota and dichotomous or quantitative clinical variables, providing a powerful and robust alternative for the current microbiome differential abundance analysis.