108 research outputs found
Metagenomic Profiling of a Microbial Assemblage Associated with the California Mussel: A Node in Networks of Carbon and Nitrogen Cycling
Mussels are conspicuous and often abundant members of rocky shores and may constitute an important site for the nitrogen cycle due to their feeding and excretion activities. We used shotgun metagenomics of the microbial community associated with the surface of mussels (Mytilus californianus) on Tatoosh Island in Washington state to test whether there is a nitrogen-based microbial assemblage associated with mussels. Analyses of both tidepool mussels and those on emergent benches revealed a diverse community of Bacteria and Archaea with approximately 31 million bp from 6 mussels in each habitat. Using MG-RAST, between 22.5–25.6% were identifiable using the SEED non-redundant database for proteins. Of those fragments that were identifiable through MG-RAST, the composition was dominated by Cyanobacteria and Alpha- and Gamma-proteobacteria. Microbial composition was highly similar between the tidepool and emergent bench mussels, suggesting similar functions across these different microhabitats. One percent of the proteins identified in each sample were related to nitrogen cycling. When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes. In some instances, the nitrogen-utilizing profile of this assemblage was more concordant with soil metagenomes in the Midwestern U.S. than for open ocean system. Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes. In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes
Meeting Report: The 2nd Annual Argonne Soils Workshop, Argonne National Laboratory, Chicago Illinois, USA, October 6-8, 2010
This report summarizes the proceedings of the 2nd Annual Argonne Soils Workshop held at Argonne National Laboratory October 6–8, 2010. The workshop assembled a diverse group of soil ecologists, microbiologists, molecular biologists, and computational scientists to discuss the challenges and opportunities related to implementation of metagenomics approaches in soil microbial ecology. The overarching theme of the workshop was “designing ecologically meaningful soil metagenomics research”, which encouraged presentations on both ecological and computational topics. The workshop fostered valuable cross-discipline communication and delivered the message that soil metagenomics research must be based on an iterative process between biological inquiry and bioinformatics tools
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation
Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Infection and Immunity 77 (2009): 2367-2375, doi:10.1128/IAI.01520-08.Shifts in microbial communities are implicated in the pathogenesis of a number of
gastrointestinal diseases, but we have limited understanding of the mechanisms
that lead to altered community structures. One difficulty with studying these
mechanisms in human subjects is the inherent baseline variability of the
microbiota in different individuals that arise due to varying life histories. To try
and overcome this baseline variability we employed a mouse model to control
host genotype, diet and other possible influences on the microbiota. This allowed
us to determine if the indigenous microbiota in such mice had a stable baseline
community structure and whether this community exhibited a consistent
response following antibiotic administration. We employed a tag sequencing
strategy targeting the V6 hypervariable region of the bacterial small-subunit (16S)
ribosomal RNA combined with massively parallel sequencing to determine the
community structure of the gut microbiota. Inbred mice in a controlled
environment harbored a reproducible baseline community that was significantly
impacted by antibiotic administration. The ability of the gut microbial community
to recover to baseline following cessation of antibiotic administration varied
according to the antibiotic regimen administered. Severe antibiotic pressure
resulted in reproducible long-lasting alterations in the gut microbial community
including a decrease in overall diversity. The finding of stereotypic responses of
the indigenous microbiota to ecologic stress implies that a better understanding
of the factors that govern community structure could lead to strategies for the
intentional manipulation of this ecosystem to preserve or restore a healthy
microbiota.The main projects were funded in whole with federal
funds from the NIAID, NIH, Department of Health and Human Services, under
contract number N01-AI-30058. Additional funding was supplied via subcontracts
from the Woods Hole Center for Oceans and Human Health from the National
Institutes of Health and National Science Foundation (NIH/NIEHS 1 P50
ES012742-01 and NSF/OCE 0430724-J. Stegeman PI to H.G.M. and M.L.S. and
R01 DK070875 to V.B.Y.) and a grants from the W.M. Keck Foundation and the
G. Unger Vetlesen Foundation (to M.L.S.). D.A.A. was supported by the National
Institutes of Health under a Ruth L. Kirschstein National Research Service Award
(T32 HL07749)
B cell depletion therapy upregulates Dkk-1 skin expression in patients with systemic sclerosis: association with enhanced resolution of skin fibrosis
Regional Mucosa-Associated Microbiota Determine Physiological Expression of TLR2 and TLR4 in Murine Colon
Many colonic mucosal genes that are highly regulated by microbial signals are differentially expressed along the rostral-caudal axis. This would suggest that differences in regional microbiota exist, particularly mucosa-associated microbes that are less likely to be transient. We therefore explored this possibility by examining the bacterial populations associated with the normal proximal and distal colonic mucosa in context of host Toll-like receptors (TLR) expression in C57BL/6J mice housed in specific pathogen-free (SPF) and germ-free (GF) environments. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis revealed significant differences in the community structure and diversity of the mucosa-associated microbiota located in the distal colon compared to proximal colon and stool, the latter two clustering closely. Differential expression of colonic TLR2 and TLR4 along the proximal-distal axis was also found in SPF mice, but not in GF mice, suggesting that enteric microbes are essential in maintaining the regional expression of these TLRs. TLR2 is more highly expressed in proximal colon and decreases in a gradient to distal while TLR4 expression is highest in distal colon and a gradient of decreased expression to proximal colon is observed. After transfaunation in GF mice, both regional colonization of mucosa-associated microbes and expression of TLRs in the mouse colon were reestablished. In addition, exposure of the distal colon to cecal (proximal) microbiota induced TLR2 expression. These results demonstrate that regional colonic mucosa-associated microbiota determine the region-specific expression of TLR2 and TLR4. Conversely, region-specific host assembly rules are essential in determining the structure and function of mucosa-associated microbial populations. We believe this type of host-microbial mutualism is pivotal to the maintenance of intestinal and immune homeostasis
Engineering of increased L-Threonine production in bacteria by combinatorial cloning and machine learning
The goal of this study is to develop a general strategy for bacterial engineering using an integrated synthetic biology and machine learning (ML) approach. This strategy was developed in the context of increasing L-threonine production in Escherichia coli ATCC 21277. A set of 16 genes was initially selected based on metabolic pathway relevance to threonine biosynthesis and used for combinatorial cloning to construct a set of 385 strains to generate training data (i.e., a range of L-threonine titers linked to each of the specific gene combinations). Hybrid (regression/classification) deep learning (DL) models were developed and used to predict additional gene combinations in subsequent rounds of combinatorial cloning for increased L-threonine production based on the training data. As a result, E. coli strains built after just three rounds of iterative combinatorial cloning and model prediction generated higher L-threonine titers (from 2.7 g/L to 8.4 g/L) than those of patented L-threonine strains being used as controls (4–5 g/L). Interesting combinations of genes in L-threonine production included deletions of the tdh, metL, dapA, and dhaM genes as well as overexpression of the pntAB, ppc, and aspC genes. Mechanistic analysis of the metabolic system constraints for the best performing constructs offers ways to improve the models by adjusting weights for specific gene combinations. Graph theory analysis of pairwise gene modifications and corresponding levels of L-threonine production also suggests additional rules that can be incorporated into future ML models
Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1
Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application in improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels
Patient-specific Bacteroides genome variants in pouchitis
© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in mBio 7 (2016): e01713-16, doi:10.1128/mBio.01713-16.A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen. Each patient harbored Bacteroides spp. that are closely related to commonly occurring clinical isolates, including Bacteroides ovatus, B. thetaiotaomicron, B. vulgatus, and B. fragilis, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique Bacteroides capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch.Leona M. and Harry B. Helmsley Charitable Trust; Bay and Paul Foundations; Frank R. Lillie Research Innovation Award; Gastrointestinal Research Foundation of Chicag
Innate and adaptive humoral responses coat distinct commensal bacteria with immunoglobulin A
Immunoglobulin A (IgA) is prominently secreted at mucosal surfaces and coats a fraction of the intestinal microbiota. However, the commensal bacteria bound by IgA are poorly characterized and the type of humoral immunity they elicit remains elusive. We used bacterial flow cytometry coupled with 16S rRNA gene sequencing (IgA-Seq) in murine models of immunodeficiency to identify IgA-bound bacteria and elucidate mechanisms of commensal IgA targeting. We found that residence in the small intestine, rather than bacterial identity, dictated induction of specific IgA. Most commensals elicited strong T-independent (TI) responses that originated from the orphan B1b lineage and from B2 cells, but excluded natural antibacterial B1a specificities. Atypical commensals including segmented filamentous bacteria and Mucispirillum evaded TI responses but elicited T-dependent IgA. These data demonstrate exquisite targeting of distinct commensal bacteria by multiple layers of humoral immunity and reveal a specialized function of the B1b lineage in TI mucosal IgA responses
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