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Noah Fierer - One of the best experts on this subject based on the ideXlab platform.

  • using network analysis to explore co occurrence patterns in soil microbial commUnities
    The ISME Journal, 2012
    Co-Authors: Albert Barberan, Scott T Bates, Emilio O Casamayor, Noah Fierer
    Abstract:

    Exploring large environmental datasets generated by high-throughput DNA sequencing technologies requires new analytical approaches to move beyond the basic inventory descriptions of the composition and diversity of natural microbial commUnities. In order to investigate potential interactions between microbial taxa, network analysis of significant taxon co-occurrence patterns may help to decipher the structure of complex microbial commUnities across spatial or temporal gradients. Here, we calculated associations between microbial taxa and applied network analysis approaches to a 16S rRNA gene barcoded pyrosequencing dataset containing >160 000 bacterial and archaeal sequences from 151 soil samples from a broad range of ecosystem types. We described the topology of the resulting network and defined Operational Taxonomic Unit categories based on abundance and occupancy (that is, habitat generalists and habitat specialists). Co-occurrence patterns were readily revealed, including general non-random association, common life history strategies at broad Taxonomic levels and unexpected relationships between commUnity members. Overall, we demonstrated the potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial commUnity structure and the ecological rules guiding commUnity assembly.

  • metagenomic and small subUnit rrna analyses reveal the genetic diversity of bacteria archaea fungi and viruses in soil
    Applied and Environmental Microbiology, 2007
    Co-Authors: Noah Fierer, Mya Breitbart, James Nulton, Peter Salamon, Catherine A Lozupone, Ryan T Jones, Michael S Robeson, Robert Edwards, Ben Felts
    Abstract:

    Recent studies have highlighted the surprising richness of soil bacterial commUnities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subUnit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an Operational Taxonomic Unit [OTU]), we found that the archaeal and fungal commUnities were consistently less even than the bacterial commUnities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral commUnities using a metagenomic approach, we found that soil viruses are Taxonomically diverse and distinct from the commUnities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal Taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.

Juan S Escobar - One of the best experts on this subject based on the ideXlab platform.

  • metformin is associated with higher relative abundance of mucin degrading akkermansia muciniphila and several short chain fatty acid producing microbiota in the gut
    Diabetes Care, 2017
    Co-Authors: Jacobo De La Cuestazuluaga, Noel T Mueller, Vanessa Corralesagudelo, Eliana P Velasquezmejia, Jenny A Carmona, Jose M Abad, Juan S Escobar
    Abstract:

    OBJECTIVE Recent studies suggest the beneficial effects of metformin on glucose metabolism may be microbially mediated. We examined the association of type 2 diabetes, metformin, and gut microbiota in commUnity-dwelling Colombian adults. On the basis of previous research, we hypothesized that metformin is associated with higher levels of short-chain fatty acid (SCFA)–producing and mucin-degrading microbiota. RESEARCH DESIGN AND METHODS Participants were selected from a larger cohort of 459 participants. The present analyses focus on the 28 participants diagnosed with diabetes—14 taking metformin— and the 84 participants without diabetes who were matched (3-to-1) to participants with diabetes by sex, age, and BMI. We measured demographic information, anthropometry, and blood biochemical parameters and collected fecal samples from which we performed 16S rRNA gene sequencing to analyze the composition and structure of the gut microbiota. RESULTS We found an association between diabetes and gut microbiota that was modified by metformin use. Compared with participants without diabetes, participants with diabetes taking metformin had higher relative abundance of Akkermansia muciniphila, a microbiota known for mucin degradation, and several gut microbiota known for production of SCFAs, including Butyrivibrio, Bifidobacterium bifidum, Megasphaera, and an Operational Taxonomic Unit of Prevotella. In contrast, compared with participants without diabetes, participants with diabetes not taking metformin had higher relative abundance of Clostridiaceae 02d06 and a distinct Operational Taxonomic Unit of Prevotella and a lower abundance of Enterococcus casseliflavus. CONCLUSIONS Our results support the hypothesis that metformin shifts gut microbiota composition through the enrichment of mucin-degrading A. muciniphila as well as several SCFA-producing microbiota. Future studies are needed to determine if these shifts mediate metformin’s glycemic and anti-inflammatory properties.

Ben Felts - One of the best experts on this subject based on the ideXlab platform.

  • metagenomic and small subUnit rrna analyses reveal the genetic diversity of bacteria archaea fungi and viruses in soil
    Applied and Environmental Microbiology, 2007
    Co-Authors: Noah Fierer, Mya Breitbart, James Nulton, Peter Salamon, Catherine A Lozupone, Ryan T Jones, Michael S Robeson, Robert Edwards, Ben Felts
    Abstract:

    Recent studies have highlighted the surprising richness of soil bacterial commUnities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subUnit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an Operational Taxonomic Unit [OTU]), we found that the archaeal and fungal commUnities were consistently less even than the bacterial commUnities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral commUnities using a metagenomic approach, we found that soil viruses are Taxonomically diverse and distinct from the commUnities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal Taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.

Jacobo De La Cuestazuluaga - One of the best experts on this subject based on the ideXlab platform.

  • metformin is associated with higher relative abundance of mucin degrading akkermansia muciniphila and several short chain fatty acid producing microbiota in the gut
    Diabetes Care, 2017
    Co-Authors: Jacobo De La Cuestazuluaga, Noel T Mueller, Vanessa Corralesagudelo, Eliana P Velasquezmejia, Jenny A Carmona, Jose M Abad, Juan S Escobar
    Abstract:

    OBJECTIVE Recent studies suggest the beneficial effects of metformin on glucose metabolism may be microbially mediated. We examined the association of type 2 diabetes, metformin, and gut microbiota in commUnity-dwelling Colombian adults. On the basis of previous research, we hypothesized that metformin is associated with higher levels of short-chain fatty acid (SCFA)–producing and mucin-degrading microbiota. RESEARCH DESIGN AND METHODS Participants were selected from a larger cohort of 459 participants. The present analyses focus on the 28 participants diagnosed with diabetes—14 taking metformin— and the 84 participants without diabetes who were matched (3-to-1) to participants with diabetes by sex, age, and BMI. We measured demographic information, anthropometry, and blood biochemical parameters and collected fecal samples from which we performed 16S rRNA gene sequencing to analyze the composition and structure of the gut microbiota. RESULTS We found an association between diabetes and gut microbiota that was modified by metformin use. Compared with participants without diabetes, participants with diabetes taking metformin had higher relative abundance of Akkermansia muciniphila, a microbiota known for mucin degradation, and several gut microbiota known for production of SCFAs, including Butyrivibrio, Bifidobacterium bifidum, Megasphaera, and an Operational Taxonomic Unit of Prevotella. In contrast, compared with participants without diabetes, participants with diabetes not taking metformin had higher relative abundance of Clostridiaceae 02d06 and a distinct Operational Taxonomic Unit of Prevotella and a lower abundance of Enterococcus casseliflavus. CONCLUSIONS Our results support the hypothesis that metformin shifts gut microbiota composition through the enrichment of mucin-degrading A. muciniphila as well as several SCFA-producing microbiota. Future studies are needed to determine if these shifts mediate metformin’s glycemic and anti-inflammatory properties.

Raeild M M Abed - One of the best experts on this subject based on the ideXlab platform.

  • Fouling Microbial CommUnities on Plastics Compared with Wood and Steel: Are They Substrate- or Location-Specific?
    Microbial Ecology, 2019
    Co-Authors: Thirumahal Muthukrishnan, Maryam Al Khaburi, Raeild M M Abed
    Abstract:

    Although marine biofouling has been widely studied on different substrates, information on biofouling on plastics in the Arabian Gulf is limited. Substrate- and location-specific effects were investigated by comparing the microbial commUnities developed on polyethylene terephthalate (PET) and polyethylene (PE) with those on steel and wood, at two locations in the Sea of Oman. Total biomass was lower on PET and PE than on steel and wood. PET had the highest bacterial abundance at both locations, whereas chlorophyll a concentrations did not vary between substrates. MiSeq 16S ribosomal RNA sequencing revealed comparable Operational Taxonomic Unit (OTU) richness on all substrates at one location but lower numbers on PET and PE at the other location. Non-metric multidimensional scaling (NMDS) showed distinct clusters of the bacterial commUnities based on substrate (analysis of similarity (ANOSIM), R = 0.45–0.97, p