Using ecological diversity measures with bacterial communities

Hill, Tom; Walsh, Kerry; Harris, J. Arthur; Moffett, Bruce F.

doi:10.1111/j.1574-6941.2003.tb01040.x

Cited by 797 publications

(465 citation statements)

References 36 publications

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“…The Shannon index provides a moderate weighting to rare and intermediate species in comparison to dominant species, making this index more sensitive to changes in abundance of rare groups than other diversity indices [27]. Diversity indices and standard deviations were calculated using EstimateS [9].…”

Section: S Rdna Sequencesmentioning

confidence: 99%

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

et al. 2004

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Understanding how microbial genotypes are arrayed in space is crucial for identifying local factors that may influence the spatial distribution of genetic diversity. In this study we investigated variation in 16S rDNA sequences and rep-PCR fingerprints of Streptomyces stains isolated from prairie soil among three locations and four soil depths. Substantial variation in Streptomyces OTU (operational taxonomic unit) and BOX-PCR fingerprint diversity was found among locations within a limited spatial area (1 m 2 ). Further, phylogenetic lineages at each location were distinct. However, there was little variation in genetic diversity among isolates from different soil depths and similar phylogenetic lineages were found at each depth. Some clones were found at a localized scale while other clones had a relatively widespread distribution. There was poor correspondence between 16S rDNA groupings and rep-PCR fingerprint groupings. The finding of distinct phylogenetic lineages and the variation in spatial distribution of clones suggests that selection pressures may vary over the soil landscape.

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Section: S Rdna Sequencesmentioning

confidence: 99%

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

et al. 2004

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“…A principal component analysis was also performed based on the T-RFLP profiles of fecal samples. Microbial diversity was calculated using the Simpson and Shannon-Wiener indexes of diversity to assess microbial community members' evenness and richness (27). The distributions of the variables were investigated with the Shapiro Wilk test.…”

Section: Methodsmentioning

confidence: 99%

The Relationship between Habitual Dietary Intake and Gut Microbiota in Young Japanese Women

Seura

Yoshino

Fukuwatari

2017

Journal of Nutritional Science and Vitaminology, J Nutr Sci Vit

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Summary Recent studies have shown that dietary content affects the health of the host by changing the gut microbiota. However, little is known about the association of microbiota composition with habitual diet in Japanese people. Here, we aimed to clarify the relationship between the fecal microbiota and habitual dietary intake of micronutrients, macronutrients and food groups in healthy young Japanese women. Analysis of fecal microbiota was performed by the terminal restriction fragment length polymorphism (T-RFLP) method, and a dietary survey was conducted over three consecutive days using a weighed food record method. T-RFLP pattern analysis divided the subjects into two clusters, where cluster A group had a high relative abundance of Bacteroides and Clostridium cluster IV, and cluster B group had a high relative abundance of Bifidobacterium and Lactobacillales. Cluster A group also had lower intakes of iron and vitamin K and higher intakes of mushrooms and snacks than cluster B group. Analysis of Spearman rank correlations found several significant relationships between fecal microbiota and intake of nutrients and food groups. Bifidobacterium was correlated with iron intake, and Clostridium cluster XI was negatively correlated with intakes of cholesterol and eggs. These results suggest that dietary habits may strongly affect Bifidobacterium, Bacteroides and Clostridium abundance in the gut microbiota of young Japanese women. This is the first study to show relationships between fecal microbiota and habitual dietary intake in Japanese people. Accumulation of results from similar studies will help to elucidate the relationships between dietary intake and diseases in Japanese people.

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“…Although soil bacterial diversity, as estimated by phylotype richness and diversity (Shannon index) [46] varied across ecosystem types, a predominance of Firmicutes clones and abundance of Bacillus species were presented in studies on alkaliphilic diversity in distinctive habitats as lakes in Mongolia and lake Van in Turkey [47].…”

Section: Phylogenetic Analysis Of the Bacterial Clones And Dominant Pmentioning

confidence: 99%

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

et al. 2015

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The Atacama Desert, one of the driest deserts in the world, represents a unique extreme environmental ecosystem to explore the bacterial diversity as it is considered to be at the dry limit for life. A 16S rRNA gene (spanning the hyper variable V3 region) library was constructed from an alkaline sample of unvegetated soil at the hyperarid margin in the Atacama Desert. A total of 244 clone sequences were used for MOTHUR analysis, which revealed 20 unique phylotypes or operational taxonomic units (OTUs). V3 region amplicons of the 16S rRNA were suitable for distinguishing the bacterial community to the genus and specie level. We found that all OTUs were affiliated with taxa representative of the Firmicutes phylum. The extremely high abundance of Firmicutes indicated that most bacteria in the soil were spore-forming survivors. In this study we detected a narrower diversity as compared to other ecological studies performed in other areas of the Atacama Desert. The reported genera were Oceanobacillus (representing the 69.5 % of the clones sequenced), Bacillus, Thalassobacillus and Virgibacillus. The present work shows physical and chemical parameters have a prominent impact on the microbial community structure. It constitutes an example of the communities adapted to live in extreme conditions caused by dryness and metal concentrations.

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Using ecological diversity measures with bacterial communities

Cited by 797 publications

References 36 publications

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

Spatial Variation in Streptomyces Genetic Composition and Diversity in a Prairie Soil

The Relationship between Habitual Dietary Intake and Gut Microbiota in Young Japanese Women

Phylogenetic Profiling and Diversity of Bacterial Communities in the Death Valley, an Extreme Habitat in the Atacama Desert

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