Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life

Analysis of the correlation between cervical HPV infection, cervical lesions and vaginal microecology

Background

Vaginal microbiota is involved in human papillomavirus (HPV) infection and cervical cancer (CC) progression, and the specific changes in vaginal microbial composition during this process remains uncertain.

Objective

This study aimed to observe the changes in the specific composition of vaginal microorganisms in different cervical lesions and identify biomarkers at different stages of lesions.

Methods

In this study we used the illumina high-throughput gene sequencing technology to determine the V4 region of 16SrRNA and observed the vaginal microbial composition in different cervical lesions.

Results

The vaginal microbiota of patients with high-risk HPV infection and cervical lesions is significantly different from that of the normal population, but there is no significant difference in the richness of vaginal microbes. The diversity of vaginal species in CC patients is higher than that in high-risk HPV infection or CIN patients. The main manifestation is an increase in the diversity of vaginal microbes, a decrease in the relative abundance of cyanobacteria and Lactobacillus, and an increase in the relative abundance of dialister, peptonephila and other miscellaneous bacteria. There are characteristic vaginal biomarker in normal women, high risk HPV patients and CC patients. In detail, the biomarker in the normal group was varibaculum, the biomarker in the high-risk HPV group was saccharopolyspora, the biomarker of the CC group was the Proteobacteria, Corynebacterium, Coprococcus, Peptococcus and Ruminococcus.

Conclusions

The study indicated that the compositions of vaginal microbes in different cervical lesions is different. The vaginal microbial composition has a certain diagnostic effect on healthy women, patients with high-risk HPV infection and cervical lesions. These microbes may serve as potential biomarkers for CC. It also provided an effective way for the treatment of HPV infections and cervical lesions.

Atopic Dermatitis: Beyond the Skin and Into the Gut

Atopic dermatitis (AD) is a common, chronic and recurring inflammatory skin disorder characterized by an intensely pruritic, eczematous dermatitis. The etiology of AD is thought to involve a combination of environmental, genetic, and immunologic factors. Emerging research has investigated factors that may impact individual risk for developing AD, disease severity, and treatment response. One component is the gut microbiome, which is considered to play an essential role in maintaining the homeostasis of several organ systems. The gut microbiome has been described as a major regulator of the "gut-skin axis," yet some studies have yielded conflicting evidence regarding the strength of the association of gut microbiota dysbiosis with AD. This review discusses recent insights into the role of the gut microbiome in AD pathogenesis and its interplay among other complex systems that govern the current assessments of and treatments for AD.

Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains

Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of "healthy" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S. anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.

Global Meta-analysis of Urine Microbiome: Colonization of Polycyclic Aromatic Hydrocarbon-degrading Bacteria Among Bladder Cancer Patients

BACKGROUND

The application of next-generation sequencing techniques has enabled characterization of urinary tract microbiome. Although many studies have demonstrated associations between the human microbiome and bladder cancer (BC), these have not always reported consistent results, thereby necessitating cross-study comparisons. Thus, the fundamental questions remain how we can utilize this knowledge.

OBJECTIVE

The aim of our study was to examine the disease-associated changes in urine microbiome communities globally utilizing a machine learning algorithm.

DESIGN, SETTING, AND PARTICIPANTS

Raw FASTQ files were downloaded for the three published studies in urinary microbiome in BC patients, in addition to our own prospectively collected cohort.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

Demultiplexing and classification were performed using the QIIME 2020.8 platform. De novo operational taxonomic units were clustered using the uCLUST algorithm and defined by 97% sequence similarity and classified at the phylum level against the Silva RNA sequence database. The metadata available from the three studies included were used to evaluate the differential abundance between BC patients and controls via a random-effect meta-analysis using the metagen R function. A machine learning analysis was performed using the SIAMCAT R package.

RESULTS AND LIMITATIONS

Our study includes 129 BC urine and 60 healthy control samples across four different countries. We identified a total of 97/548 genera to be differentially abundant in the BC urine microbiome compared with that of healthy patients. Overall, while the differences in diversity metrics were clustered around the country of origin (Kruskal-Wallis, p < 0.001), collection methodology was a driver of microbiome composition. When assessing dataset from China, Hungary, and Croatia, data demonstrated no discrimination capacity to distinguish between BC patients and healthy adults (area under the curve [AUC] 0.577). However, inclusion of samples with catheterized urine improved the diagnostic accuracy of prediction for BC to AUC 0.995, with precision-recall AUC = 0.994. Through elimination of contaminants associated with the collection methodology among all cohorts, our study identified increased abundance of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria Sphingomonas, Acinetobacter, Micrococcus, Pseudomonas, and Ralstonia to be consistently present in BC patients.

CONCLUSIONS

The microbiota of the BC population may be a reflection of PAH exposure from smoking, environmental pollutants, and ingestion. Presence of PAHs in the urine of BC patients may allow for a unique metabolic niche and provide necessary metabolic resources where other bacteria are not able to flourish. Furthermore, we found that while compositional differences are associated with geography more than with disease, many are driven by the collection methodology.

PATIENT SUMMARY

The goal of our study was to compare the urine microbiome of bladder cancer patients with that of healthy controls and evaluate any potential bacteria that may be more likely to be found in patients with bladder cancer. Our study is unique as it evaluates this across multiple countries, to find a common pattern. After we removed some of the contamination, we were able to localize several key bacteria that are more likely to be found in the urine of bladder cancer patients. These bacteria all share their ability to break down tobacco carcinogens.

An Altered Skin and Gut Microbiota Are Involved in the Modulation of Itch in Atopic Dermatitis

Skin and gut microbiota play an important role in the pathogenesis of atopic dermatitis (AD). An alteration of the microbiota diversity modulates the development and course of AD, e.g., decreased microbiome diversity correlates with disease severity, particularly in lesional skin of AD. Itch is a hallmark of AD with unsatisfying treatment until now. Recent evidence suggests a possible role of microbiota in altering itch in AD through gut-skin-brain interactions. The microbial metabolites, proinflammatory cytokines, and impaired immune response lead to a modulation of histamine-independent itch, disruption of epidermal barrier, and central sensitization of itch mechanisms. The positive impact of probiotics in alleviating itch in AD supports this hypothesis, which may lead to novel strategies for managing itchy skin in AD patients. This review summarizes the emerging findings on the correlation between an altered microbiota and gut-skin-brain axis in AD, especially in modulating itchy skin.

Human circulating bacteria and dysbiosis in non-infectious diseases

Blood microorganisms were once thought to indicate infection. Blood in healthy people appears to be devoid of growing bacteria; nonetheless, intracellular dormant forms of bacteria have been reported previously. With breakthroughs in sequencing and bioinformatics, the presence of bacterial DNA in healthy human blood initiated the controversy of human blood microbiota (HBM). Recently, bacteria-specific DNA and culturable bacteria were found in healthy human blood. Researchers wanted to study the phenomena of a "healthy blood microbiota" by providing a thorough description of bacterially produced nucleic acids using many complementing molecular and traditional microbiological approaches. Because blood is a relatively limited and particular environment, culturability and plate count issues can be overcome using enhanced cultured procedures. However, more evidence is required to confirm that healthy human blood contains normal microbiota. Cavities, mouth and intestinal microbiota, trauma, surgery, and animal/insect bites can introduce bacteria into human blood. All these factors strengthen the concept of transient blood bacteria too. The presence of blood bacteria may be caused by temporary immunological clearance and absorption by dendritic or M cells. This review provides an extensive and comprehensive analysis that suggests that healthy blood bacteria may not be typical microbiota but transient circulatory microorganisms. In this study, we look at how contaminants (Escherichia, Shigella, Pseudomonads, etc.) from the skin, laboratory environments, and reagents can affect the interpretation of blood-derived microbial information and the relationship between the circulating bacteria and non-communicable diseases. Circulating transient bacteria may play a role in the pathogenesis of non-infectious diseases such as diabetes and CVD. Contamination-free hematological studies can aid in understanding the disease mechanisms, therapy, and biomarkers.

Faecal microbiome and metabolic signatures in rectal neuroendocrine tumors

Background: The prevalence of rectal neuroendocrine tumors (RNET) has increased substantially over the past decades. Little is known on mechanistic alteration in the pathogenesis of such disease. We postulate that perturbations of human gut microbiome-metabolome interface influentially affect the development of RNET. The study aims to characterize the composition and function of faecal microbiome and metabolites in RNET individuals. Methods: We performed deep shotgun metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling of faecal samples from the discovery cohort (18 RNET patients, 40 controls), and validated the microbiome and metabolite-based classifiers in an independent cohort (15 RNET participants, 19 controls). Results: We uncovered a dysbiotic gut ecological microenvironment in RNET patients, characterized by aberrant depletion and attenuated connection of microbial species, and abnormally aggregated lipids and lipid-like molecules. Functional characterization based on our in-house and Human Project Unified Metabolic Analysis Network 2 (HUMAnN2) pipelines further indicated a nutrient deficient gut microenvironment in RNET individuals, evidenced by diminished activities such as energy metabolism, vitamin biosynthesis and transportation. By integrating these data, we revealed 291 robust associations between representative differentially abundant taxonomic species and metabolites, indicating a tight interaction of gut microbiome with metabolites in RNET pathogenesis. Finally, we identified a cluster of gut microbiome and metabolite-based signatures, and replicated them in an independent cohort, showing accurate prediction of such neoplasm from healthy people. Conclusions: Our current study is the first to comprehensively characterize the perturbed interface of gut microbiome and metabolites in RNET patients, which may provide promising targets for microbiome-based diagnostics and therapies for this disorder.

Interaction between four galactans with different structural characteristics and gut microbiota

Human gut microbiota played a key role in maintaining and regulating host health. Gut microbiota composition could be altered by daily diet and related nutrients. Diet polysaccharide, an important dietary nutrient, was one kind of biological macromolecules linked by the glycosidic bonds. Galactans were widely used in foods due to their gelling, thickening and stabilizing properties. Recently, effects of different galactans on gut microbiota have attracted much attention. This review described the structural characteristics of 4 kinds of galactans, including porphyran, agarose, carrageenan, and arabinogalactan, along with the effects of different galactans on gut microbiota and production of short-chain fatty acids. The ability of gut microbiota to utilize galactans with different structural characteristics and related degradation mechanism were also summarized. All these four galactans could be used by gut Bacteroides. Besides, the porphyran could be utilized by Lactobacillus and Bifidobacterium, while the arabinogalactan could be utilized by Lactobacillus, Bifidobacterium and Roseburia. Four galactans with significant difference in molecular weight/degree of polymerization, glycosidic linkage, esterification, branching and monosaccharide composition required gut microbes which could utilize them have corresponding genes encoding the corresponding enzymes for decomposition. This review could help to understand the relationship between galactans with different structural characteristics and gut microbiota, and provide information for potential use of galactans as functional foods.

How the Gut Microbiome Links to Menopause and Obesity, with Possible Implications for Endometrial Cancer Development

Background: Interest is growing in the dynamic role of gut microbiome disturbances in human health and disease. No direct evidence is yet available to link gut microbiome dysbiosis to endometrial cancer. This review aims to understand any association between microbiome dysbiosis and important risk factors of endometrial cancer, high estrogen levels, postmenopause and obesity. Methods: A systematic search was performed with PubMed as primary database. Three separate searches were performed to identify all relevant studies. Results: Fifteen studies were identified as highly relevant and included in the review. Eight articles focused on the relationship with obesity and eight studies focused on the menopausal change or estrogen levels. Due to the heterogeneity in patient populations and outcome measures, no meta-analysis could be performed. Both the menopausal change and obesity were noted to enhance dysbiosis by reducing microbiome diversity and increasing the Firmicutes to Bacteroidetes ratio. Both also incurred estrobolome changes, leading to increased systemic estrogen levels, especially after menopause. Furthermore, microbiome dysbiosis was reported to be related to systemic inflammation through toll-like receptor signaling deficiencies and overexpression of pro-inflammatory cytokines. Conclusions: This review highlights that the female gut microbiome is intrinsically linked to estrogen levels, menopausal state and systemic inflammation, which indicates gut microbiome dysbiosis as a potential hallmark for risk stratification for endometrial cancer. Studies are needed to further define the role the gut microbiome plays in women at risk for endometrial cancer.

Sponge microbiome stability during environmental acquisition of highly specific photosymbionts

In this study, we used in situ transplantations to provide the first evidence of horizontal acquisition of cyanobacterial symbionts by a marine sponge. The acquisition of the symbionts by the host sponge Petrosia ficiformis, which was observed in distinct visible patches, appeared several months after transplantation and at different times on different sponge specimens. We further used 16S rRNA gene amplicon sequencing of genomic DNA (gDNA) and complementary DNA (cDNA) and metatranscriptomics to investigate how the acquisition of the symbiotic cyanobacterium Candidatus Synechococcus feldmannii perturbed the diverse microbiota associated with the host P. ficiformis. To our surprise, the microbiota remained relatively stable during cyanobacterial symbiont acquisition at both structural (gDNA content) and activity (cDNA expression) levels. At the transcriptomic level, photosynthesis was the primary function gained following the acquisition of cyanobacteria. Genes involved in carotene production and oxidative stress tolerance were among those highly expressed by Ca. S. feldmannii, suggesting that this symbiont may protect itself and its host from damaging light radiation.

Comparing Gut Microbiome in Mothers' Own Breast Milk- and Formula-Fed Moderate-Late Preterm Infants

Gut microbiome plays an important role in adult human health and diseases. However, how nutritional factors shape the initial colonization of gut bacteria in infants, especially in preterm infants, is still not completely known. In this study, we compared the effects of feeding with mothers' own breast milk (MBM) and formula on the initial composition and gene expression of gut bacteria in moderate-late preterm infants. Fecal samples were collected from ten formula-fed and ten MBM healthy infants born between 32 and 37 weeks' gestation after they reached full-volume enteral feedings. Total DNAs were extracted from fecal samples for amplicon sequencing of 16S ribosomal RNA (rRNA) gene and total RNA with rRNA depletion for metatranscriptome RNA-Seq 16S rRNA gene amplicon sequencing results showed that the alpha-diversity was similar between the MBM- and formula-fed preterm infants, but the beta-diversity showed a significant difference in composition (p = 0.002). The most abundant taxa were Veillonella (18.4%) and Escherichia/Shigella (15.2%) in MBM infants, whereas the most abundant taxa of formula-fed infants were Streptococcus (18.6%) and Klebsiella (17.4%). The genera Propionibacterium, Streptococcus, and Finegoldia and order Clostridiales had significantly higher relative abundance in the MBM group than the formula group, whereas bacteria under family Enterobacteriaceae, genera Enterococcus and Veillonella, and class Bacilli were more abundant in the formula group. In general, microbiomes from both diet groups exhibited high functional levels of catalytic activity and metabolic processing when analyzed for gene ontology using a comparative metatranscriptome approach. Statistically, the microbial genes in the MBM group had an upregulation in expression related to glycine reductase, periplasmic acid stress response in Enterobacteria, acid resistance mechanisms, and L-fucose utilization. In contrast, the formula-fed group had upregulations in genes associated with methionine and valine degradation functions. Our data suggest that the nutritional source plays a role in shaping the moderate-late preterm gut microbiome as evidenced by the differences in bacterial composition and gene expression profiles in the fecal samples. The MBM group enriched Propionibacterium. Glycine reductase was highly upregulated in the microbiota from MBM along with the upregulated acid stress tolerance genes, suggesting that the intensity of fermentation process was enhanced.

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut

Microbes alter their transcriptomic profiles in response to the environment. The physiological conditions experienced by a microbial community can thus be inferred using meta-transcriptomic sequencing by comparing transcription levels of specifically chosen genes. However, this analysis requires accurate reference genomes to identify the specific genes from which RNA reads originate. In addition, such an analysis should avoid biases in transcript counts related to differences in organism abundance. In this study we describe an approach to address these difficulties. Sample-specific meta-genomic assembled genomes (MAGs) were used as reference genomes to accurately identify the origin of RNA reads, and transcript ratios of genes with opposite transcription responses were compared to eliminate biases related to differences in organismal abundance, an approach hereafter named the "diametric ratio" method. We used this approach to probe the environmental conditions experienced by Escherichia spp. in the gut of 4 premature infants, 2 of whom developed necrotizing enterocolitis (NEC), a severe inflammatory intestinal disease. We analyzed twenty fecal samples taken from four premature infants (4-6 time points from each infant), and found significantly higher diametric ratios of genes associated with low oxygen levels in samples of infants later diagnosed with NEC than in samples without NEC. We also show this method can be used for examining other physiological conditions, such as exposure to nitric oxide and osmotic pressure. These study results should be treated with caution, due to the presence of confounding factors that might also distinguish between NEC and control infants. Nevertheless, together with benchmarking analyses, we show here that the diametric ratio approach can be applied for evaluating the physiological conditions experienced by microbes in situ. Results from similar studies can be further applied for designing diagnostic methods to detect NEC in its early developmental stages.

Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome

Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.

Antibiotic resistance genes in the Actinobacteria phylum

The Actinobacteria phylum is one of the oldest bacterial phyla that have a significant role in medicine and biotechnology. There are a lot of genera in this phylum that are causing various types of infections in humans, animals, and plants. As well as antimicrobial agents that are used in medicine for infections treatment or prevention of infections, they have been discovered of various genera in this phylum. To date, resistance to antibiotics is rising in different regions of the world and this is a global health threat. The main purpose of this review is the molecular evolution of antibiotic resistance in the Actinobacteria phylum.

Gut microbiota development of preterm infants hospitalised in intensive care units

Gut microbiome development affects infant health and postnatal physiology. The gut microbe assemblages of preterm infants have been reported to be different from that of healthy term infants. However, the patterns of ecosystem development and inter-individual differences remain poorly understood. We investigated hospitalised preterm infant gut microbiota development using 16S rRNA gene amplicons and the metabolic profiles of 268 stool samples obtained from 17 intensive care and 42 term infants to elucidate the dynamics and equilibria of the developing microbiota. Infant gut microbiota were predominated by Gram-positive cocci, Enterobacteriaceae or Bifidobacteriaceae, which showed sequential transitions to Bifidobacteriaceae-dominated microbiota. In neonatal intensive care unit preterm infants (NICU preterm infants), Staphylococcaceae abundance was higher immediately after birth than in healthy term infants, and Bifidobacteriaceae colonisation tended to be delayed. No specific NICU-cared infant enterotype-like cluster was observed, suggesting that the constrained environment only affected the pace of transition, but not infant gut microbiota equilibrium. Moreover, infants with Bifidobacteriaceae-dominated microbiota showed higher acetate concentrations and lower pH, which have been associated with host health. Our data provides an in-depth understanding of gut microbiota development in NICU preterm infants and complements earlier studies. Understanding the patterns and inter-individual differences of the preterm infant gut ecosystem is the first step towards controlling the risk of diseases in premature infants by targeting intestinal microbiota.

The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD)

NAFLD is currently the main cause of chronic liver disease in developed countries, and the number of NAFLD patients is growing worldwide. NAFLD often has similar symptoms to other metabolic disorders, including type 2 diabetes and obesity. Recently, the role of the gut microbiota in the pathophysiology of many diseases has been revealed. Regarding NAFLD, experiments using gut microbiota transplants to germ-free animal models showed that fatty liver disease development is determined by gut bacteria. Moreover, the perturbation of the composition of the gut microbiota has been observed in patients suffering from NAFLD. Numerous mechanisms relating the gut microbiome to NAFLD have been proposed, including the dysbiosis-induced dysregulation of gut endothelial barrier function that allows for the translocation of bacterial components and leads to hepatic inflammation. In addition, the various metabolites produced by the gut microbiota may impact the liver and thus modulate NAFLD susceptibility. Therefore, the manipulation of the gut microbiome by probiotics, prebiotics or synbiotics was shown to improve liver phenotype in NAFLD patients as well as in rodent models. Hence, further knowledge about the interactions among dysbiosis, environmental factors, and diet and their impacts on the gut-liver axis can improve the treatment of this life-threatening liver disease and its related disorders.

What is new and relevant for sequencing-based microbiome research? A mini-review

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Sample storage and nucleic acid isolation influence microbiota compositions.

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Error-corrected amplicon sequence variants (ASVs) improve 16S rRNA analysis.

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Contamination and host cells confound and complicate microbiota analysis.

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Quantitative and active microbiota analyses can complement existing methods.

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Open data and protocol sharing increases transparency and reproducibility.

Microbiome research has transformed the scientific landscape, as reflected by the exponential increase in microbiome-related publications from many different disciplines. Host-associated microbial communities play a role for almost all aspects of human, animal and plant biology and health. Consequently, there are tremendous expectations for the development of new clinical, agricultural and biotechnological applications of microbiome research. However, the field continues to be largely shaped by descriptive studies, the mechanistic understanding of microbiome functions for their hosts remains fragmentary, and direct applications of microbiome research are lacking. The aim of this review is therefore to provide a general introduction to the technical opportunities and challenges of microbiome research, as well as to make experimental and bioinformatic recommendations, i.e. (i) to avoid, reduce and assess the confounding effects of sample storage, nucleic acid isolation and microbial contamination; (ii) to minimize non-microbial contributions in host-associated microbiome samples; (iii) to sharpen the focus on physiologically relevant microbiome features by distinguishing signals from metabolically active and inactive or dead microbes and by adopting quantitative methods; and (iv) to enforce open data and protocol policies in order increase the transparency, reproducibility and credibility of the field.

Effects of early life NICU stress on the developing gut microbiome

Succession of gut microbial community structure for newborns is highly influenced by early life factors. Many preterm infants cared for in the NICU are exposed to parent-infant separation, stress, and pain from medical care procedures. The purpose of the study was to investigate the impact of early life stress on the trajectory of gut microbial structure. Stool samples from very preterm infants were collected weekly for 6 weeks. NICU stress exposure data were collected daily for 6 weeks. V4 region of the 16S rRNA gene was amplified by PCR and sequenced. Zero-inflated beta regression model with random effects was used to assess the impact of stress on gut microbiome trajectories. Week of sampling was significant for Escherichia, Staphylococcus, Enterococcus, Bifidobacterium, Proteus, Streptococcus, Clostridium butyricum, and Clostridium perfringens. Antibiotic usage was significant for Proteus, Citrobacter, and C. perfringens. Gender was significant for Proteus. Stress exposure occurring 1 and 2 weeks prior to sampling had a significant effect on Proteus and Veillonella. NICU stress exposure had a significant effect on Proteus and Veillonella. An overall dominance of Gammaproteobacteria was found. Findings suggest early life NICU stress may significantly influence the developing gut microbiome, which is important to NICU practice and future microbiome research.

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat

Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.

Regulation of Microbiota by Vitamin D Receptor: A Nuclear Weapon in Metabolic Diseases

Metabolic syndrome is a multi-faceted disease. The microbiota, as a newly discovered organ, contributes to the pathogenesis and progression of metabolic syndrome. Recent studies have demonstrated that nuclear receptors play critical roles in metabolic diseases. In the current review, we discuss the general role of the microbiome in health and metabolic syndrome. We summarize the functions of the nuclear receptor vitamin D receptor (VDR) in metabolism. The focus of this review is the novel roles of vitamin D/VDR signaling in regulating inflammation and the microbiome, especially in obesity. Furthermore, we extend our discussion of potential gut-liver axis mediated by VDR signaling and microbiota in obesity. Finally, we discuss the potential clinical application of probiotics and fecal microbiota transplantation in prevention and treatment of metabolic syndrome. Insights into nuclear receptors in metabolism and metabolic diseases will allow us to develop new strategies for fighting metabolic diseases.

Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles

During the first weeks of life, microbial colonization of the gut impacts human immune system maturation and other developmental processes. In premature infants, aberrant colonization has been implicated in the onset of necrotizing enterocolitis (NEC), a life-threatening intestinal disease. To study the premature infant gut colonization process, genome-resolved metagenomics was conducted on 343 fecal samples collected during the first 3 months of life from 35 premature infants housed in a neonatal intensive care unit, 14 of whom developed NEC, and metaproteomic measurements were made on 87 samples. Microbial community composition and proteomic profiles remained relatively stable on the time scale of a week, but the proteome was more variable. Although genetically similar organisms colonized many infants, most infants were colonized by distinct strains with metabolic profiles that could be distinguished using metaproteomics. Microbiome composition correlated with infant, antibiotics administration, and NEC diagnosis. Communities were found to cluster into seven primary types, and community type switched within infants, sometimes multiple times. Interestingly, some communities sampled from the same infant at subsequent time points clustered with those of other infants. In some cases, switches preceded onset of NEC; however, no species or community type could account for NEC across the majority of infants. In addition to a correlation of protein abundances with organism replication rates, we found that organism proteomes correlated with overall community composition. Thus, this genome-resolved proteomics study demonstrated that the contributions of individual organisms to microbiome development depend on microbial community context.IMPORTANCE Humans are colonized by microbes at birth, a process that is important to health and development. However, much remains to be known about the fine-scale microbial dynamics that occur during the colonization period. We conducted a genome-resolved study of microbial community composition, replication rates, and proteomes during the first 3 months of life of both healthy and sick premature infants. Infants were found to be colonized by similar microbes, but each underwent a distinct colonization trajectory. Interestingly, related microbes colonizing different infants were found to have distinct proteomes, indicating that microbiome function is not only driven by which organisms are present, but also largely depends on microbial responses to the unique set of physiological conditions in the infant gut.

Prevalence and Source of Fecal and Oral Bacteria on Infant, Child, and Adult Hands

Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of both fecal and oral origins are commonly found on hands. It also establishes that the uniqueness of fecal and oral bacterial communities across people can allow for determination of the likely individual from whom the fecal and oral bacteria came. These techniques allow for understanding the hands as a vector for microbial transmission within families and across populations, which has important implications for public health.

Modern hygienic practices are applied to avoid exposure to pathogens that spread via fecal-oral transmission. Despite this, the gastrointestinal tract is quickly colonized by fecal microbes. The hands are an important vector for the transmission of microbes, but the frequency at which fecal and oral microbes exist on hands and the source of those microbes have not been extensively described. Using data from a previous study that characterized the fecal, oral, and skin microbiota from 73 families, we found a significant incidence of fecal and oral microbes on hands. Of palms, 48.9% had fecal signal and 67.2% had oral signal. Fecal, oral, and forehead microbes were tracked to family members and an individual’s own palms far more often than to unrelated individuals and showed relationships with age, gender, and parental status. For instance, oral microbes that were specifically sourced to the same individual (oneself) were most common on infant palms; mothers had more infant-child-sourced and oral-sourced microbes on their palms than nonparents. Fecal microbes on palms more often sourced to members of the family than unrelated individuals, but more often to other members of the family than oneself. This study supports that the hands are an important vector for the transfer of fecal and oral microbes within families.

IMPORTANCE Bacteria live all around us, and we are constantly exposed to them during our everyday lives. Modern standards of hygiene aim to limit exposure to fecal bacteria, and yet bacteria rapidly colonize the gut in early life and following antibacterial treatment. Exposures to fecal and oral microbes provide risk of disease, but are also necessary since commensal microbes play important roles in health. This work establishes that bacteria of both fecal and oral origins are commonly found on hands. It also establishes that the uniqueness of fecal and oral bacterial communities across people can allow for determination of the likely individual from whom the fecal and oral bacteria came. These techniques allow for understanding the hands as a vector for microbial transmission within families and across populations, which has important implications for public health.

Microbiome and Gut Dysbiosis

The gastrointestinal (GI) tract is the residence of trillions of microorganisms that include bacteria, archaea, fungi and viruses. The collective genomes of whole microbial communities (microbiota) integrate the gut microbiome. Up to 100 genera and 1000 distinct bacterial species were identified in digestive tube niches. Gut microbiomes exert permanent pivotal functions by promoting food digestion, xenobiotic metabolism and regulation of innate and adaptive immunological processes. Proteins, peptides and metabolites released locally and at distant sites trigger many cell signalling and pathways. This intense crosstalk maintains the host-microbial homeostasis. Diet, age, diet, stress and diseases cause increases or decreases in relative abundance and diversity bacterial specie of GI and other body sites. Studies in animal models and humans have shown that a persistent imbalance of gut's microbial community, named dysbiosis, relates to inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), diabetes, obesity, cancer, cardiovascular and central nervous system disorders. Notably specific bacterial communities are promising clinical target to treat inflammatory and infectious diseases. In this context, intestinal microbiota transplantation (IMT) is one optional treatment for IBD, in particular to patients with recurrent Clostridium difficile-induced pseudo-membrane colitis. Here we discuss on recent discoveries linking whole gut microbiome dysbiosis to metabolic and inflammatory diseases and potential prophylactic and therapeutic applications of faecal and phage therapy, probiotic and prebiotic diets.

Impact of prematurity and nutrition on the developing gut microbiome and preterm infant growth

BACKGROUND

Identification of factors that influence the neonatal gut microbiome is urgently needed to guide clinical practices that support growth of healthy preterm infants. Here, we examined the influence of nutrition and common practices on the gut microbiota and growth in a cohort of preterm infants.

RESULTS

With weekly gut microbiota samples spanning postmenstrual age (PMA) 24 to 46 weeks, we developed two models to test associations between the microbiota, nutrition and growth: a categorical model with three successive microbiota phases (P1, P2, and P3) and a model with two periods (early and late PMA) defined by microbiota composition and PMA, respectively. The more significant associations with phase led us to use a phase-based framework for the majority of our analyses. Phase transitions were characterized by rapid shifts in the microbiota, with transition out of P1 occurring nearly simultaneously with the change from meconium to normal stool. The rate of phase progression was positively associated with gestational age at birth, and delayed transition to a P3 microbiota was associated with growth failure. We found distinct bacterial metabolic functions in P1-3 and significant associations between nutrition, microbiota phase, and infant growth.

CONCLUSION

The phase-dependent impact of nutrition on infant growth along with phase-specific metabolic functions suggests a pioneering potential for improving growth outcomes by tailoring nutrient intake to microbiota phase.

Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut

Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. While much is known about the evolution of Escherichia coli in controlled laboratory environments, less effort has been made to elucidate the genome dynamics of E. coli in its native settings. Here, we follow the genome dynamics of co-existing E. coli lineages in situ of the infant gut during the first year of life. One E. coli lineage causes a urinary tract infection (UTI) and experiences several alterations of its genomic content during subsequent antibiotic treatment. Interestingly, all isolates of this uropathogenic E. coli strain carried a highly stable plasmid implicated in virulence of diverse pathogenic strains from all over the world. While virulence elements are certainly beneficial during infection scenarios, their role in gut colonization and pathogen persistence is poorly understood. We performed in vivo competitive fitness experiments to assess the role of this highly disseminated virulence plasmid in gut colonization, but found no evidence for a direct benefit of plasmid carriage. Through plasmid stability assays, we demonstrate that this plasmid is maintained in a parasitic manner, by strong first-line inheritance mechanisms, acting on the single-cell level, rather than providing a direct survival advantage in the gut. Investigating the ecology of endemic accessory genetic elements, in their pathogenic hosts and native environment, is of vital importance if we want to understand the evolution and persistence of highly virulent and drug resistant bacterial isolates.

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling

The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those of Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo gene expression of vertically transmitted microbes and found that transmitted strains of Bacteroides and Bifidobacterium species were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development. IMPORTANCE Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events. Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.

Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics

One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments. On the other hand, the output of whole metagenomic shotgun sequencing is mixture of short DNA fragments belonging to various genomes, therefore this approach requires more sophisticated computational algorithms for clustering of related sequences, commonly referred to as sequence binning. There are currently two types of binning methods: taxonomy dependent and taxonomy independent. The first type classifies the DNA fragments by performing a standard homology inference against a reference database, while the latter performs the reference-free binning by applying clustering techniques on features extracted from the sequences. In this review, we describe the strategies within the second approach. Although these strategies do not require prior knowledge, they have higher demands on the length of sequences. Besides their basic principle, an overview of particular methods and tools is provided. Furthermore, the review covers the utilization of the methods in context with the length of sequences and discusses the needs for metagenomic data preprocessing in form of initial assembly prior to binning.

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by which microbiome perturbation can cause a phenotypic change in the patient. The direct approach for the analysis of the functional capacity of the microbiome is via shotgun metagenomics. An inexpensive method to estimate the functional capacity of a microbial community is through collecting 16S rRNA gene profiles then indirectly inferring the abundance of functional genes. This inference approach has been implemented in the PICRUSt and Tax4Fun software tools. However, those tools have important limitations since they rely on outdated functional databases and uncertain phylogenetic trees and require very specific data pre-processing protocols. Here we introduce Piphillin, a straightforward algorithm independent of any proposed phylogenetic tree, leveraging contemporary functional databases and not obliged to any singular data pre-processing protocol. When all three inference tools were evaluated against actual shotgun metagenomics, Piphillin was superior in predicting gene composition in human clinical samples compared to both PICRUSt and Tax4Fun (p<0.01 and p<0.001, respectively) and Piphillin’s ability to predict disease associations with specific gene orthologs exhibited a 15% increase in balanced accuracy compared to PICRUSt. From laboratory animal samples, no performance advantage was observed for any one of the tools over the others and for environmental samples all produced unsatisfactory predictions. Our results demonstrate that functional inference using the direct method implemented in Piphillin is preferable for clinical biospecimens. Piphillin is publicly available for academic use at http://secondgenome.com/Piphillin.

Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants

The potentially critical stage of initial gut colonization in premature infants occurs in the hospital environment, where infants are exposed to a variety of hospital-associated bacteria. Because few studies of microbial communities are strain-resolved, we know little about the extent to which specific strains persist in the hospital environment and disperse among infants. To study this, we compared 304 near-complete genomes reconstructed from fecal samples of 21 infants hospitalized in the same intensive care unit in two cohorts, over 3 years apart. The genomes represent 159 distinct bacterial strains, only 14 of which occurred in multiple infants. Enterococcus faecalis and Staphylococcus epidermidis, common infant gut colonists, exhibit diversity comparable to that of reference strains, inline with introduction of strains from infant-specific sources rather than a hospital strain pool. Unlike other infants, a pair of sibling infants shared multiple strains, even after extensive antibiotic administration, suggesting overlapping strain-sources and/or genetic selection drive microbiota similarities. Interestingly, however, five strains were detected in infants hospitalized three years apart. Three of these were also detected in multiple infants in the same year. This finding of a few widely dispersed and persistent bacterial colonizers despite overall low potential for strain dispersal among infants has implications for understanding and directing healthy colonization.

Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates

Necrotizing enterocolitis (NEC) remains a devastating intestinal disease in preterm neonates. In this population, disruption of the gut microbiota development, mainly due to organ immaturity, antibiotic use and hospital microbial environment, plays a key role in the pathogenesis of NEC. This gut dysbiosis has been associated with opportunistic pathogens overgrowth, expression of virulence factors, altered metabolic functions and inflammatory dysregulated responses. In this review, we provide an updated summary of the host and gut microbiota interactions during the formative early life. We also explore the key determinants of gut dysbiosis in preterm neonates with NEC. Finally, we discuss the promising role of bacteriotherapy in the management of NEC, the aim being to shape or restore the beneficial gut bacterial communities.

Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches

The human body is the residence of a large number of commensal (non-pathogenic) and pathogenic microbial species that have co-evolved with the human genome, adaptive immune system, and diet. With recent advances in DNA-based technologies, we initiated the exploration of bacterial gene functions and their role in human health. The main goal of the human microbiome project is to characterize the abundance, diversity and functionality of the genes present in all microorganisms that permanently live in different sites of the human body. The gut microbiota expresses over 3.3 million bacterial genes, while the human genome expresses only 20 thousand genes. Microbe gene-products exert pivotal functions via the regulation of food digestion and immune system development. Studies are confirming that manipulation of non-pathogenic bacterial strains in the host can stimulate the recovery of the immune response to pathogenic bacteria causing diseases. Different approaches, including the use of nutraceutics (prebiotics and probiotics) as well as phages engineered with CRISPR/Cas systems and quorum sensing systems have been developed as new therapies for controlling dysbiosis (alterations in microbial community) and common diseases (e.g., diabetes and obesity). The designing and production of pharmaceuticals based on our own body’s microbiome is an emerging field and is rapidly growing to be fully explored in the near future. This review provides an outlook on recent findings on the human microbiomes, their impact on health and diseases, and on the development of targeted therapies.

Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case

Microbial colonization of the human gastrointestinal tract plays an important role in establishing health and homeostasis. However, the time-dependent functional signatures of microbial and human proteins during early colonization of the gut have yet to be determined. To this end, we employed shotgun proteomics to simultaneously monitor microbial and human proteins in fecal samples from a preterm infant during the first month of life. Microbial community complexity increased over time, with compositional changes that were consistent with previous metagenomic and rRNA gene data. More specifically, the function of the microbial community initially involved biomass growth, protein production, and lipid metabolism, and then switched to more complex metabolic functions, such as carbohydrate metabolism, once the community stabilized and matured. Human proteins detected included those responsible for epithelial barrier function and antimicrobial activity. Some neutrophil-derived proteins increased in abundance early in the study period, suggesting activation of the innate immune system. Likewise, abundances of cytoskeletal and mucin proteins increased later in the time course, suggestive of subsequent adjustment to the increased microbial load. This study provides the first snapshot of coordinated human and microbial protein expression in a preterm infant's gut during early development.

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads.

Extensive strain-level copy-number variation across human gut microbiome species

Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear. Here, we present a comprehensive large-scale analysis of intra-species copy-number variation in the gut microbiome, introducing a rigorous computational pipeline for detecting such variation directly from shotgun metagenomic data. We uncover a large set of variable genes in numerous species and demonstrate that this variation has significant functional and clinically relevant implications. We additionally infer intra-species compositional profiles, identifying population structure shifts and the presence of yet uncharacterized variants. Our results highlight the complex relationship between microbiome composition and functional capacity, linking metagenome-level compositional shifts to strain-level variation.

Draft Genome Sequence of Clostridium butyricum Strain NOR 33234, Isolated from an Elderly Patient with Diarrhea

Clostridium butyricum is one of the species frequently present in patients’ stool samples. However, the identification of this species is sometimes difficult. Here, we present the draft genome of Clostridium butyricum NOR 33234, which was isolated from a patient with suspected Clostridium difficile infection-associated diarrhea and resembles Clostridium clostridioforme in biochemical tests.

Systems-based approaches to unravel multi-species microbial community functioning

Some of the most transformative discoveries promising to enable the resolution of this century's grand societal challenges will most likely arise from environmental science and particularly environmental microbiology and biotechnology. Understanding how microbes interact in situ, and how microbial communities respond to environmental changes remains an enormous challenge for science. Systems biology offers a powerful experimental strategy to tackle the exciting task of deciphering microbial interactions. In this framework, entire microbial communities are considered as metaorganisms and each level of biological information (DNA, RNA, proteins and metabolites) is investigated along with in situ environmental characteristics. In this way, systems biology can help unravel the interactions between the different parts of an ecosystem ultimately responsible for its emergent properties. Indeed each level of biological information provides a different level of characterisation of the microbial communities. Metagenomics, metatranscriptomics, metaproteomics, metabolomics and SIP-omics can be employed to investigate collectively microbial community structure, potential, function, activity and interactions. Omics approaches are enabled by high-throughput 21st century technologies and this review will discuss how their implementation has revolutionised our understanding of microbial communities.

Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome

The human gut microbiome is a major contributor to human metabolism and health, yet the metabolic processes that are carried out by various community members, the way these members interact with each other and with the host, and the impact of such interactions on the overall metabolic machinery of the microbiome have not yet been mapped. Here, we discuss recent efforts to study the metabolic inner workings of this complex ecosystem. We will specifically highlight two interrelated lines of work, the first aiming to deconvolve the microbiome and to characterize the metabolic capacity of various microbiome species and the second aiming to utilize computational modeling to infer and study metabolic interactions between these species.

Development of the preterm infant gut microbiome: a research priority

The very low birth weight (VLBW) infant is at great risk for marked dysbiosis of the gut microbiome due to multiple factors, including physiological immaturity and prenatal/postnatal influences that disrupt the development of a normal gut flora. However, little is known about the developmental succession of the microbiota in preterm infants as they grow and mature. This review provides a synthesis of our understanding of the normal development of the infant gut microbiome and contrasts this with dysbiotic development in the VLBW infant. The role of human milk in normal gut microbial development is emphasized, along with the role of the gut microbiome in immune development and gastroenteric health. Current research provides evidence that the gut microbiome interacts extensively with many physiological systems and metabolic processes in the developing infant. However, to the best of our knowledge, there are currently no studies prospectively mapping the gut microbiome of VLBW infants through early childhood. This knowledge gap must be filled to inform a healthcare system that can provide for the growth, health, and development of VLBW infants. The paper concludes with speculation about how the VLBW infants' gut microbiome might function through host-microbe interactions to contribute to the sequelae of preterm birth, including its influence on growth, development, and general health of the infant host.