Biology subjects

Eren, A. M.

Publications and source records attributed to Eren, A. M..

45 records · Page 3Linked to original sources

bioRxiv2020

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity

BackgroundThe increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale. ResultsHere, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes revealed distinct genomic groups based on shared genome content. H. parainfluenzae genomes separated into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identified an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulated species-level taxonomy and habitat preferences. However, while most R. mucilaginosa were restricted to the tongue as expected, two genomes represented a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identified not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences were absent or ubiquitous. ConclusionsOur findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.

microbiology↗

bioRxiv2020

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and their intriguing patterns of site specificity amidst the lack of dispersal limitation. Yet, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among the taxa that belong to recently discovered branches of microbial life. Here we assembled metagenomes from daily tongue and dental plaque samples from multiple individuals and reconstructed 790 non-redundant genomes, 43 of which resolved to TM7 that formed six monophyletic clades distinctly associated either with plaque or with tongue. Both pangenomic and phylogenomic analyses grouped tongue-specific TM7 clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 grouped together with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and the mobilome of the cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of human associated microbes. Additionally, we report that prophages are widespread amongst oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.

microbiology↗

bioRxiv2020

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis

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 emergence of pathobionts or loss/lack of essential microbes needed for appropriate immunological education, our findings suggest the latter. A dominant Bacteroides strain absent following antibiotic-induced perturbation was cultivated from murine fecal samples. Addition of this strain into mice with antibiotic-induced dysbiosis significantly promoted immune tolerance and reduced incidence of colitis in IL-10-/- mice, but only if engrafted early in life, and not during adulthood. Thus, key members of the gut microbiome are essential for development of immune tolerance to commensal microbes in early life and their addition in presence of gut dysbiosis during this period can reduce colitis risk in genetically prone hosts. HighlightsO_LISpecific gut microbes promote early life immune tolerance to key commensal microbes C_LIO_LILoss of early life keystone microbes increases colitis risk in genetically prone hosts C_LIO_LIEmergence of absent commensal microbes late in life worsened colitis outcome C_LIO_LIEarly life exposure to a missing keystone Bacteroides strain reduced colitis risk C_LI

microbiology↗

bioRxiv2019

Disinfection exhibits systematic impacts on the drinking water microbiome.

Limiting microbial growth during drinking water distribution is achieved either by maintaining a disinfectant residual or through nutrient limitation without the use of a disinfectant. The impact of these contrasting approaches on the drinking water microbiome is not systematically understood. We utilized genome-resolved metagenomics to compare the structure, metabolic traits, and population genomes of drinking water microbiomes across multiple full-scale drinking water systems utilizing these two-distinct microbial growth control strategies. Microbial communities cluster together at the structural- and functional potential-level based on the presence or absence of a disinfectant residual. Disinfectant residual concentrations alone explained 17 and 6.5% of the variance in structure and functional potential of the drinking water microbiome, respectively, despite including samples from multiple drinking water systems with variable source waters and source water communities, treatment strategies, and chemical compositions. The drinking water microbiome is structurally and functionally less diverse and less variable across disinfected systems as compared to non-disinfected systems. While bacteria were the most abundant domain, archaea and eukaryota were more abundant in non-disinfected and disinfected systems, respectively. Community-level differences in functional potential were driven by enrichment of genes associated with carbon and nitrogen fixation in non-disinfected systems and {gamma}-aminobutyrate metabolism in disinfected systems which may be associated with the recycling of amino acids. Metagenome-assembled genome-level analyses for a subset of phylogenetically related microorganisms suggests that disinfection may select for microorganisms capable of using fatty acids, presumably from microbial decay products, via the glyoxylate cycle. Overall, we find that disinfection exhibits systematic and consistent selective pressures on the drinking water microbiome and may select for microorganisms able to utilize microbial decay products originating from disinfection inactivated microorganisms.

microbiology↗

bioRxiv2019

Accurate and Complete Genomes from Metagenomes

Genomes are an integral component of the biological information about an organism and, logically, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs), but gaps, local assembly errors, chimeras and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and in some cases achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of ~7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. Interestingly, analysis of cumulative GC skew identified potential mis-assemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

microbiology↗

bioRxiv2019

Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance.

Antimicrobial resistance (AMR) in drinking water has received less attention than counterparts in the urban water cycle. While culture-based techniques or gene-centric PCR have been used to probe the impact of treatment approaches (e.g., disinfection) on AMR in drinking water, to our knowledge there is no systematic comparison of AMR traits between disinfected and disinfectant residual-free drinking water systems. We use metagenomics to assess the associations between disinfectant residuals and AMR prevalence and its host association in full-scale drinking water distribution systems (DWDSs). The differences in AMR profiles between DWDSs are associated with the presence or absence of disinfectant. Further, AMR genes and mechanisms enriched in disinfected systems are associated with drug classes primarily linked to nontuberculous mycobacteria (NTM). Finally, evaluation of metagenome assembled genomes (MAGs) of NTM indicates that they possess AMR genes conferring intrinsic resistance to key antibiotics, whereas such NTM genomes were not detected in disinfectant residual free DWDSs. Thus, disinfection may not only influence the AMR profiles of the drinking water microbiome but also select for NTM with intrinsic AMR.

microbiology↗

bioRxiv2017

The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection

The diversity and geographical distribution of populations within major marine microbial lineages are largely governed by temperature and its co-variables. However, neither the mechanisms by which genomic heterogeneity emerges within a single population nor how it drives the partitioning of ecological niches are well understood. Here we took advantage of billions of metagenomic reads to study one of the most abundant and widespread microbial populations in the surface ocean. We characterized its substantial amount of genomic heterogeneity using single-amino acid variants (SAAVs), and identified systematic purifying selection and adaptive mechanisms governing non-synonymous variation within this population. Our Deep Learning analysis of SAAVs across metagenomes revealed two main ecological niches that reflect large-scale oceanic current temperatures, as well as six proteotypes demarcating finer-resolved niches. We identified significantly more protein variants in cold currents and an increased number of protein sweeps in warm currents, exposing a global pattern of alternating genomic diversity for this SAR11 population as it drifts along with surface ocean currents. Overall, the geographic partitioning of SAAVs suggests natural selection, rather than neutral evolution, is the main driver of the evolution of SAR11 in surface oceans.

microbiology↗

bioRxiv2017

Nitrogen-Fixing Populations Of Planctomycetes And Proteobacteria Are Abundant In The Surface Ocean

Nitrogen fixation in the surface ocean impacts the global climate by regulating the microbial primary productivity and the sequestration of carbon through the biological pump. Cyanobacterial populations have long been thought to represent the main suppliers of the bio-available nitrogen in this habitat. However, recent molecular surveys of nitrogenase reductase gene revealed the existence of rare non-cyanobacterial populations that can also fix nitrogen. Here, we characterize for the first time the genomic content of some of these heterotrophic bacterial diazotrophs (HBDs) inhabiting the open surface ocean waters. They represent new lineages within Planctomycetes and Proteobacteria, a phylum never linked to nitrogen fixation prior to this study. HBDs were surprisingly abundant in the Pacific Ocean and the Atlantic Ocean northwest, conflicting with decades of PCR surveys. The abundance and widespread occurrence of non-cyanobacterial diazotrophs in the surface ocean emphasizes the need to re-evaluate their role in the nitrogen cycle and primary productivity.

microbiology↗

bioRxiv2016

High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the recipient gut, and the widely used approaches to study the microbial ecology of FMT experiments fail to provide enough resolution to identify populations that are likely responsible for FMT-derived benefits. Here we used shotgun metagenomics to reconstruct 97 metagenome-assembled genomes (MAGs) from fecal samples of a single donor and followed their distribution in two FMT recipients to identify microbial populations with different colonization properties. Our analysis of the occurrence and distribution patterns post-FMT revealed that 22% of the MAGs transferred from the donor to both recipients and remained abundant in their guts for at least eight weeks. Most MAGs that successfully colonized the recipient gut belonged to the order Bacteroidales. The vast majority of those that lacked evidence of colonization belonged to the order Clostridiales and colonization success was negatively correlated with the number of genes related to sporulation. Although our dataset showed a link between taxonomy and the ability of a MAG to colonize the recipient gut, we also identified MAGs with different colonization properties that belong to the same taxon, highlighting the importance of genome-resolved approaches to explore the functional basis of colonization and to identify targets for cultivation, hypothesis generation, and testing in model systems for mechanistic insights.

microbiology↗