Mitchell Sogin

MBL · Josephine Bay Paul Center for Comparative Molecular Biology and Evolution

Subsurface environments are among Earth’s largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and w...

The exchange of antibiotic production and resistance genes between microorganisms can lead to the emergence of new pathogens. In this study, short-read mapping of metagenomic samples taken over time from the illeal pouch of a patient with ulcerative colitis to a Bacteroides fragilis metagenome-assembled genome revealed two distinct genomic arrangem...

Bile acids (BAs) are cholesterol-derived molecules that aid in digestion and nutrient absorption, regulate host metabolic processes, and influence physiology of the gut microbiota. Both the host and its microbiome contribute to enzymatic modifications that shape the chemical diversity of BAs in the gut. Several bacterial species have been reported...

Bacteroides fragilis comprises 1%–5% of the gut microbiota in healthy humans but can expand to >50% of the population in ulcerative colitis (UC) patients experiencing inflammation. The mechanisms underlying such microbial blooms are poorly understood, but the gut of UC patients has physicochemical features that differ from healthy patients and like...

Inflammatory bowel diseases (IBD) arise from a convergence of underlying genetic susceptibility, environmental factors, and shifts in gut microbiota function and membership. Although the latter may trigger and contribute to IBD, there is little consensus on a specific causative pathogen. In this study, we demonstrate that commensal Bacteroides frag...

The anthozoan sea anemone Nematostella vectensis belongs to the phylum of cnidarians which also includes jellyfish and corals. Nematostella are native to United States East Coast marsh lands, where they constantly adapt to changes in salinity, temperature, oxygen concentration and pH. Its natural ability to continually acclimate to changing environ...

Background & Aims Perturbations in the early life gut microbiome are associated with increased risk for complex immune disorders like inflammatory bowel diseases. We previously showed maternal antibiotic-induced gut dysbiosis vertically transmitted to offspring increases experimental colitis risk in IL-10 gene deficient (IL-10-/-) mice, a finding t...

Perturbations in the early life gut microbiome are associated with increased risk to complex immune disorder like inflammatory bowel diseases. We previously showed maternal antibiotic-induced gut dysbiosis vertically passed to offspring increases experimental colitis risk in IL-10 gene deficient (IL-10 −/− ) mice. While this could arise from emerge...

The design and performance characteristics of municipal drinking water systems can profoundly influence public health. To assess the operational attributes of an Accra, Ghana drinking water distribution system, high-throughput 454 pyrosequencing was employed to characterize its bacterial community composition. Samples from the waterworks and four h...

Objective: To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life. Design: Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS). Settings: Rural New Hampshire, USA. Population or sample: Two hundred and sixty-six full-term infants...

Arsenic is a ubiquitous environmental toxicant with antimicrobial properties that can be found in food and drinking water. The influence of arsenic exposure on the composition of the human microbiome in US populations remains unknown, particularly during the vulnerable infant period. We investigated the relationship between arsenic exposure and gut...

Here, we report an approach to detect diverse bacterial and fungal taxa in complex samples by direct analysis of community RNA in one step using NanoString probe sets. We designed rRNA-targeting probe sets to detect 42 bacterial and fungal genera or species common in cystic fibrosis (CF) sputum and demonstrated the taxon specificity of these probes...

Background: The impact of degree of prematurity at birth on premature infant gut microbiota has not been extensively studied in comparison to term infants in large cohorts. Methods: To determine the effect of gestational age at birth and postnatal exposures on gut bacterial colonization in infants, we analyzed 65 stool samples from 17 premature...

Cambridge Core - Computational Science and Modelling - Planets and Life - edited by Woodruff T. Sullivan, III

Earth’s subsurface environment is one of the largest, yet least studied, biomes on Earth, and many questions remain regarding what microorganisms are indigenous to the subsurface. Through the activity of the Census of Deep Life (CoDL) and the Deep Carbon Observatory, an open access 16S ribosomal RNA gene sequence database from diverse subsurface en...

A list of common contaminants previously identified as putative contaminants.

Synechococcus are ubiquitous and cosmopolitan cyanobacteria that play important roles in global productivity and biogeochemical cycles. This study investigated the fine scale microdiversity, seasonal patterns, and spatial distributions of Synechococcus in estuarine waters of Little Sippewissett salt marsh (LSM) on Cape Cod, MA. The proportion of Sy...

Background: Ulcerative colitis (UC) only involves the colonic mucosa. Yet, nearly 50% of patients with UC who undergo total proctocolectomy with ileal pouch anal anastomosis develop UC-like inflammation of the ileal pouch (pouchitis). By contrast, patients with familial adenomatous polyposis (FAP) with ileal pouch anal anastomosis develop pouchiti...

Importance: This longitudinal study provides an opportunity to describe shifts in the microbiomes of individual patients who suffer from ulcerative colitis (UC) prior to and following inflammation. Pouchitis serves as a model for UC with a predictable incidence of disease onset and enables prospective longitudinal investigations of UC etiology pri...

Box-and-whisker plots for the percent relative abundance of Bacteroides. Samples were taken from pouches that never develop inflammation (N), were in an inflamed state (I), after antibiotic treatment (A), and without inflammation (W samples). The relative abundance was calculated using three distinct measures: 16S marker gene (GAST), short-read tax...

Cultivar detection throughout longitudinal sampling using shotgun metagenomic sequences. To determine whether a cultivar isolated from an individual was present throughout the longitudinal sampling, we mapped each of the shotgun metagenomic data sets for the patient back to the cultivar assembly. The figure displays mean coverage for 2-kbp sections...

Abundant Bacteroides oligotypes and MAGs isolated from pouchitis patients during inflammation. The letters a to e indicate unique Bacteroides MED oligotypes detected during inflammation with “na” indicating samples not available from visits during inflammation. Taxonomy of the oligotype is based on similarity to hits in the NCBI RefSeq rRNA databas...

Relative abundance of taxa (GAST assignments). The heat map displays the percent relative abundance of genera within each sample based on 16S marker genes. GAST assigned taxonomy to each of the reads. The tree was constructed by average linkage using the Bray-Curtis dissimilarity matrix of the percent relative abundance matrix of genera within each...

A cluster dendrogram based on MG-RAST functional annotation of each shotgun metagenomic data set. Clustering is based on Ward’s minimum variance of a Bray-Curtis dissimilarity matrix derived from the relative abundance of functions. A function was assigned if the read matched at 80% of the length and the hit achieved a maximum E value of 10−15. The...

Clinical metadata for each sample. The sample name indicates pouchitis (p) or nonpouchitis (n) patients, patient ID, visit number, luminal aspirate (M) versus mucosal-brush (GG) sampling site, and the number of days after pouch functionalization. The condition of the pouch and the results of clinical examination of the patient and what treatment (i...

Summary of linear mixed-effects model results. The coefficients predicted by the linear mixed-effects model for relative abundance of each genus and oligotype in this study are shown. The 97.5% confidence intervals for each coefficient are reported as coef_lwr (coef stands for coefficient, and lwr stands for lower) (2.5%) and coef_upr (upr stands f...

Functional cluster dendrogram of all Bacteroides MAGs. Functional classification of each genome is according to RAST, and the distance among the genomes was calculated using Ward’s minimum variance of a Bray-Curtis dissimilarity matrix derived from the relative abundance of functions. The number of HMM hits for each of the genes within the CPS and...

Summary of MAGs recovered from each patient. The summary includes the patient ID, unique MAG ID, taxonomy, summary of the MAG size, common assembly statistics, and completion/contamination based on three bacterial single-copy core gene references. Taxonomy is based on the most common hit of the MAG contigs to genomes in the RAST database. Supplemen...

Functions of high- and low-coverage regions of p214 B. fragilis genome within HMPDACC samples. The table is supplemental to Fig. S6 and details the functions identified within the rainbow-highlighted regions of the figure. The number recorded in the first column “bin” corresponds with the number adjacent to the highlighted region of the figure. The...

Characterizing the community structure of naturally occurring microbes through marker gene amplicons has gained widespread acceptance for profiling microbial populations. The 16S ribosomal RNA (rRNA) gene provides a suitable target for most studies since (1) it meets the criteria for robust markers of evolution, e.g., both conserved and rapidly evo...

Importance: Subseafloor sediment provides a wonderful opportunity to investigate drivers of microbial diversity in communities that may be isolated for millions of years. Our manuscript shows the impact of in situ conditions on bacterial community structure in subseafloor sediment. Specifically, it shows that bacterial richness in subseafloor sedi...

With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging technique...

Gut dysbiosis, host genetics, and environmental triggers are implicated as causative factors in inflammatory bowel disease (IBD), yet mechanistic insights are lacking. Longitudinal analysis of ulcerative colitis patients following total colectomy with ileal anal anastomosis (IPAA) where >50% develop pouchitis, offers a unique setting to examine cau...

Individuals with cystic fibrosis (CF) often acquire chronic lung infections that lead to irreversible damage. We sought to examine regional variation in the microbial communities in the lungs of individuals with mild-to-moderate CF lung disease, to examine the relationship between the local microbiota and local damage, and to determine the relation...

Illumina analysis of the fungal ITS1 sequences amplified from total DNA isolated from a subset of lung-derived samples. The numbers represent the absolute number of reads on the left and the relative abundance in percent on the right from each sample. Reads were given a taxonomic assignment using VAMPS (www.vamps.mbl.edu). The database selected was...

Rank abundance analysis of the less abundant taxa in BAL, PB and scope wash samples. In this analysis, the known CF associated pathogens Stenotrophomonas, Staphylococcus, Pseudomonas, Haemophilus and Achromobacter were removed from the BAL, PB and “scope wash” sample data to allow for a focus on the minor taxa (as described in the Methods). Rank ab...

Components of the Brody score. Presented are the total Brody scores of the three right lobes of the study subjects, including the scores for each component of the Brody score that evaluate changes in bronchiectasis, peribronchial wall thickening (PB thickening), mucus plugging (Mucus), air trapping and parenchymal involvement (Parenchyma) in the lu...

Illumina analysis of the bacterial 16S rRNA sequences amplified from total DNA isolated from lung-derived and scope wash samples. The numbers represent the absolute number of reads (left) and the relative abundance in percent (right) for each sample. Reads were given a taxonomic assignment using VAMPS (www.vamps.mbl.edu). The database selected was...

Chemical dispersants are applied to oil-contaminated areas as a primary response to oceanic oil spills. The impacts of dispersants on microbial community composition and activity, particularly hydrocarbon turnover, are debated. Kleindienst et al. (1) demonstrated that Corexit 9500, a dispersant, can suppress the activity of oil-degrading microorgan...

The coalescence of next generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineating host-microbial associations has applied benefits ranging from clinical treatments to protecting our nat...

Importance The intestinal microbiome plays a critical role in infant development, and delivery mode and feeding method (breast milk vs formula) are determinants of its composition. However, the importance of delivery mode beyond the first days of life is unknown, and studies of associations between infant feeding and microbiome composition have be...

Significance Oil spills are a significant source of hydrocarbon inputs into the ocean. In response to oil spills, chemical dispersants are applied to the oil-contaminated seawater to disperse surface slicks into smaller droplets that are presumed to be more bioavailable to microorganisms. We provide evidence that chemical dispersants applied to eit...

Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex...

We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4-v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450...

Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but human and other animal gut microbiota contain an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and non-human fecal sources, we compared the V6 region of t...

Comprehensive analysis of shotgun metagenomic assemblies have revolutionized molecular microbial ecology, but few microbiologists command the full suite of bioinformatics skills necessary to process, interact, organize and visualize overlapping DNA sequence contigs. Here we introduce anvi'o, an advanced analysis and visualization platform for 'omic...

The Deepwater Horizon (DWH) oil well blowout generated an enormous plume of dispersed hydrocarbons that substantially altered the Gulf of Mexico's deep-sea microbial community. A significant enrichment of distinct microbial populations was observed, yet, little is known about the abundance and richness of specific microbial ecotypes involved in gas...

Comprehensive analysis of shotgun metagenomic assemblies have revolutionized molecular microbial ecology, but few microbiologists command the full suite of bioinformatics skills necessary to process, interact, organize and visualize overlapping DNA sequence contigs. Here we introduce anvi’o, an advanced analysis and visualization platform for ‘omic...

Unlabelled: Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from...

Objective: To test the hypothesis that maternal complications significantly affect gut colonization patterns in very low birth weight infants. Methods: Forty-nine serial stool samples were obtained weekly from nine extremely premature infants enrolled in a prospective longitudinal study. Sequencing of the bacterial 16S rRNA gene from stool sampl...

Human-associated microbial communities include fungi, but we understand little about which fungal species are present, their relative and absolute abundances, and how antimicrobial therapy impacts fungal communities. The disease cystic fibrosis (CF) often involves chronic airway colonization by bacteria and fungi, and these infections cause irrever...

Molecular microbial ecology investigations often employ large marker gene datasets, for example, ribosomal RNAs, to represent the occurrence of single-cell genomes in microbial communities. Massively parallel DNA sequencing technologies enable extensive surveys of marker gene libraries that sometimes include nearly identical sequences. Computationa...

The deep-sea hydrothermal vent habitat hosts a diverse community of archaea and bacteria that withstand extreme fluctuations in environmental conditions. Abundant viruses in these systems, a high proportion of which are lysogenic, must also withstand these environmental extremes. Here, we explore the evolutionary strategies of both microorganisms a...

Whereas a significant role for intestinal microbiota in affecting the pathogenesis and progression of chronic hepatic diseases is well documented, the contribution of the intestinal flora to acute liver injury has not been extensively addressed. Elucidating the influence of the intestinal microbiota on acute liver inflammation would be important fo...

Delineating differences in gut microbiomes of human and animal hosts contributes towards understanding human health and enables new strategies for detecting reservoirs of waterborne human pathogens. We focused upon Blautia, a single microbial genus that is important for nutrient assimilation as preliminary work suggested host-related patterns withi...