Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects

Detection of Human Y Chromosome and the SRY Gene in Fecal Samples of Female Patients Following Fecal Microbiota Transplantation

Background and Aims

We have postulated that fecal microbiota transplantation (FMT) is associated with transfer of microbiota from the donor and engraftment of intestinal epithelial cells in the recipient's colonic mucosa enabling the restoration of a stable microbial environment.

Methods

We analyzed the presence of human Y chromosome (ChrY) and sex-determining region Y (SRY) gene within total human DNA extracted from fecal samples collected from 30 donors and 22 recurrent Clostridium difficile infection (RCDI) patients before and up to 24 months after FMT. A next-generation sequencing data analysis pipeline was applied to quantify the percentage of reads aligning to human ChrY. SRY gene detection was also performed by quantitative polymerase chain reaction and droplet digital polymerase chain reaction.

Results

A significantly higher percentage of ChrY reads were identified in fecal samples of male donors as compared to female donor (P < .0001). Fecal samples collected from female RCDI patients who received FMT from male donors showed a significantly (P < .05) higher percentage of ChrY reads compared to female samples without male FMT donors. Four female patients with RCDI who received FMT from male donors showed a very large percent ChrY increase post-FMT even several months after FMT. SRY gene signal was detected by droplet digital polymerase chain reaction in 7 of the 11 fecal samples collected from the male donor pool but none from the female pool.

Conclusion

These observations clearly demonstrate the presence of ChrY and SRY gene signal in stool samples collected from male patients. The presence of increased ChrY in the stool samples of female RCDI patients after FMT from a male donor suggests possible engraftment of exfoliated intestinal epithelial cells in a subset of these patients.

Metapresence: a tool for accurate species detection in metagenomics based on the genome-wide distribution of mapping reads

Shotgun metagenomics allows comprehensive sampling of the genomic information of microbes in a given environment and is a tool of choice for studying complex microbial systems. Mapping sequencing reads against a set of reference or metagenome-assembled genomes is in principle a simple and powerful approach to define the species-level composition of the microbial community under investigation. However, despite the widespread use of this approach, there is no established way to properly interpret the alignment results, with arbitrary relative abundance thresholds being routinely used to discriminate between present and absent species. Such an approach can be affected by significant biases, especially in the identification of rare species. Therefore, it is important to develop new metrics to overcome these biases. Here, we present Metapresence, a new tool to perform reliable identification of the species in metagenomic samples based on the distribution of mapped reads on the reference genomes. The analysis is based on two metrics describing the breadth of coverage and the genomic distance between consecutive reads. We demonstrate the high precision and wide applicability of the tool using data from various synthetic communities, a real mock community, and the gut microbiome of healthy individuals and antibiotic-associated-diarrhea patients. Overall, our results suggest that the proposed approach has a robust performance in hard-to-analyze microbial communities containing contaminated or closely related genomes in low abundance.IMPORTANCEDespite the prevalent use of genome-centric alignment-based methods to characterize microbial community composition, there lacks a standardized approach for accurately identifying the species within a sample. Currently, arbitrary relative abundance thresholds are commonly employed for this purpose. However, due to the inherent complexity of genome structure and biases associated with genome-centric approaches, this practice tends to be imprecise. Notably, it introduces significant biases, particularly in the identification of rare species. The method presented here addresses these limitations and contributes significantly to overcoming inaccuracies in precisely defining community composition, especially when dealing with rare members.

Rational Design of Live Biotherapeutic Products for the Prevention of Clostridioides difficile Infection

Clostridioides difficile infection (CDI) is one of the leading causes of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) has emerged as a promising therapy for recurrent CDI, its exact mechanisms of action and long-term safety are not fully understood. Defined consortia of clonal bacterial isolates, known as live biotherapeutic products (LBPs), have been proposed as an alternative therapeutic option. However, the rational design of LBPs remains challenging. Here, we employ a computational pipeline and three independent metagenomic datasets to systematically identify microbial strains that have the potential to inhibit CDI. We first constructed the CDI-related microbial genome catalog, comprising 3,741 non-redundant metagenome-assembled genomes (nrMAGs) at the strain level. We then identified multiple potential protective nrMAGs that can be candidates for the design of microbial consortia targeting CDI, including strains from Dorea formicigenerans, Oscillibacter welbionis, and Faecalibacterium prausnitzii. Importantly, some of these potential protective nrMAGs were found to play an important role in the success of FMT, and the majority of the top protective nrMAGs can be validated by various previously reported findings. Our results demonstrate a computational framework for the rational selection of microbial strains targeting CDI, paving the way for the computational design of microbial consortia against other enteric infections.

Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome

Studies on fecal microbiota transplantation (FMT) have reported inconsistent connections between clinical outcomes and donor strain engraftment. Analyses of subspecies-level crosstalk and its influences on lineage transfer in metagenomic FMT datasets have proved challenging, as single-nucleotide polymorphisms (SNPs) are generally not linked and are often absent. Here, we utilized species genome bin (SGB), which employs co-abundance binning, to investigate subspecies-level microbiome dynamics in patients with autism spectrum disorder (ASD) who had gastrointestinal comorbidities and underwent encapsulated FMT (Chinese Clinical Trial: 2100043906). We found that interactions between donor and recipient microbes, which were overwhelmingly phylogenetically divergent, were important for subspecies transfer and positive clinical outcomes. Additionally, a donor-recipient SGB match was indicative of a high likelihood of strain transfer. Importantly, these ecodynamics were shared across FMT datasets encompassing multiple diseases. Collectively, these findings provide detailed insight into specific microbial interactions and dynamics that determine FMT success.

Principles and Terminology for Host-Microbiome-Drug Interactions

Interactions between the microbiome and medical therapies are distinct and bidirectional. The existing term "pharmacomicrobiomics" describes the effects of the microbiome on drug distribution, metabolism, efficacy, and toxicity. We propose that the term "pharmacoecology" be used to describe the effects that drugs and other medical interventions such as probiotics have on microbiome composition and function. We suggest that the terms are complementary but distinct and that both are potentially important when assessing drug safety and efficacy as well as drug-microbiome interactions. As a proof of principle, we describe the ways in which these concepts apply to antimicrobial and non-antimicrobial medications.

Limosilactobacillus reuteri administration alters the gut-brain-behavior axis in a sex-dependent manner in socially monogamous prairie voles

Research on the role of gut microbiota in behavior has grown dramatically. The probiotic L. reuteri can alter social and stress-related behaviors - yet, the underlying mechanisms remain largely unknown. Although traditional laboratory rodents provide a foundation for examining the role of L. reuteri on the gut-brain axis, they do not naturally display a wide variety of social behaviors. Using the highly-social, monogamous prairie vole (Microtus ochrogaster), we examined the effects of L. reuteri administration on behaviors, neurochemical marker expression, and gut-microbiome composition. Females, but not males, treated with live L. reuteri displayed lower levels of social affiliation compared to those treated with heat-killed L. reuteri. Overall, females displayed a lower level of anxiety-like behaviors than males. Live L. reuteri-treated females had lower expression of corticotrophin releasing factor (CRF) and CRF type-2-receptor in the nucleus accumbens, and lower vasopressin 1a-receptor in the paraventricular nucleus of the hypothalamus (PVN), but increased CRF in the PVN. There were both baseline sex differences and sex-by-treatment differences in gut microbiome composition. Live L. reuteri increased the abundance of several taxa, including Enterobacteriaceae, Lachnospiraceae NK4A136, and Treponema. Interestingly, heat-killed L. reuteri increased abundance of the beneficial taxa Bifidobacteriaceae and Blautia. There were significant correlations between changes in microbiota, brain neurochemical markers, and behaviors. Our data indicate that L. reuteri impacts gut microbiota, gut-brain axis and behaviors in a sex-specific manner in socially-monogamous prairie voles. This demonstrates the utility of the prairie vole model for further examining causal impacts of microbiome on brain and behavior.

The person-to-person transmission landscape of the gut and oral microbiomes

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

Gut microbiome health and dysbiosis: A clinical primer

The gut microbiome has been referred to as the "forgotten organ." Although much about the gut microbiome remains incompletely understood, data on its clinical importance is emerging at rapid speed. Many practicing clinicians may be unaware of the essential role that the microbiome plays in both health and disease. This review aims to improve clinical understanding of the gut microbiome by discussing key terminology and foundational concepts. The role of a healthy microbiome in normal host function is described, as well as the consequences of a disrupted microbiome (i.e., dysbiosis). Management strategies to restore the gut microbiome from a disrupted to a healthy state are also briefly discussed. Lastly, we review emerging areas for therapeutic potential and opportunity to bring determinants of microbiome health from the bench to bedside.

Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection

Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.

Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota

Sulfated glycans are ubiquitous nutrient sources for microbial communities that have coevolved with eukaryotic hosts. Bacteria metabolize sulfated glycans by deploying carbohydrate sulfatases that remove sulfate esters. Despite the biological importance of sulfatases, the mechanisms underlying their ability to recognize their glycan substrate remain poorly understood. Here, we use structural biology to determine how sulfatases from the human gut microbiota recognize sulfated glycans. We reveal seven new carbohydrate sulfatase structures spanning four S1 sulfatase subfamilies. Structures of S1_16 and S1_46 represent novel structures of these subfamilies. Structures of S1_11 and S1_15 demonstrate how non-conserved regions of the protein drive specificity toward related but distinct glycan targets. Collectively, these data reveal that carbohydrate sulfatases are highly selective for the glycan component of their substrate. These data provide new approaches for probing sulfated glycan metabolism while revealing the roles carbohydrate sulfatases play in host glycan catabolism.

Dynamics of gut microbiota during pregnancy in women with TPOAb-positive subclinical hypothyroidism: a prospective cohort study

Background

Anti-thyroid peroxidase antibody (TPOAb) positivity can contribute to inhibit thyroxine synthesis. Gut microbiota can interact with metabolic or immune diseases. However, dynamics of gut microbiota from the second (T2) to the third trimester (T3) in women with TPOAb-positive/negative subclinical hypothyroidism (TPOAb⁺/TPOAb⁻ SCH) have not been reported. Therefore, we aimed to evaluate whether gut microbiota can be potential therapeutic targets for managing TPOAb⁺ SCH.

Methods

In this single-center prospective cohort study, we observed gut microbiota dynamics by sequencing 16S rRNA from fecal samples collected in T2 (20–23^+ 6 weeks) and T3 (28–33^+ 6 weeks). TPOAb⁺/TPOAb⁻ SCH were stratified depending on whether or not they used levothyroxine (LT₄) during the pregnancy (LT₄⁺/LT₄⁻). Microbiome bioinformatics analyses were performed using QIIME2. The linear discriminant analysis effect size (LEfSe) was used for the quantitative analysis of biomarkers. Functional profiling was performed with PICRUSt2.

Results

Distinct gut microbiota dynamics from T2 to T3 were noted in the TPOAb⁻ (n = 68) and TPOAb⁺ (n = 64) SCH groups. The TPOAb⁺ LT₄⁻ group was characterized by enriched bacterial amplicon sequence variants (ASVs) of Prevotella in T2 and Bacteria, Lachnospirales, Lachnospiraceae, Blautia, and Agathobacter in T3 and by depleted ASVs of Gammaproteobacteria, Enterobacterales, and Enterobacteriaceae in T2 and Actinobacteriota, Coriobacteriia, Actinobacteria, Coriobacteriales, Bifidobacteriales, Bifidobacteriaceae, Bifidobacterium, Dorea formicigenerans, and Bifidobacterium longum in T3. The TPOAb⁺ LT₄⁺ group was characterized by enriched bacterial ASVs of Blautia, Streptococcus salivarius, and Bifidobacterium longum in T3 and by depleted ASVs of Bacteroidota, Bacteroidia, Bacteroidales, and Prevotella in T2 and Agathobacter in T3. Moreover, we identified 53 kinds of metabolic functions that were mainly involved in sugar, lipid, and amino acid metabolism.

Conclusions

Our results indicated that low dynamics of gut microbiota composition and high dynamics of its metabolic function from T2 to T3 were associated with TPOAb⁺ SCH. We concluded that gut microbiota could be new targets for treatment of TPOAb⁺ SCH during pregnancy.

Trial registration

This study was retrospectively registered at the Chinese Clinical Trial Registry (registration number ChiCTR2100047175) on June 10, 2021.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12884-022-04923-5.

Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects

Fecal microbiota transplantation (FMT) is currently used for treating Clostridium difficile infection and explored for other clinical applications in experimental trials. However, the effectiveness of this therapy could vary, and partly depend on the donor's bacterial species engraftment, whose evaluation is challenging because there are no cost-effective strategies for accurately tracking the microbe transference. In this regard, the precise identification of bacterial species inhabiting the human gut is essential to define their role in human health unambiguously. We used Nanopore-based device to sequence bacterial rrn operons (16S-ITS-23S) and to reveal species-level abundance changes in the human gut microbiota of a FMT trial. By assessing the donor and recipient microbiota before and after FMT, we further evaluated whether this molecular approach reveals strain-level genetic variation to demonstrate microbe transfer and engraftment. Strict control over sequencing data quality and major microbiota covariates was critical for accurately estimating the changes in gut microbial species abundance in the recipients after FMT. We detected strain-level variation via single-nucleotide variants (SNVs) at rrn regions in a species-specific manner. We showed that it was possible to explore successfully the donor-bacterial strain (e.g., Parabacteroides merdae) engraftment in recipients of the FMT by assessing the nucleotide frequencies at rrn-associated SNVs. Our findings indicate that the engraftment of donors' microbiota is to some extent correlated with the improvement of metabolic health in recipients and that parameters such as the baseline gut microbiota configuration, sex, and age of donors should be considered to ensure the success of FMT in humans. The study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).