Metagenomic Approach to Bacterial Diversity and Lipolytic Enzymes’ Genes from a Steam Soil of Los Humeros Geothermal Field (Puebla, México)

Wiraswati SM, Wahyudi AT, Rusmana I, Nawangsih AA. 2018. TRFLP analysis for revealing the diversity of rice phyllospherebacteria. Biodiversitas 19: 1743-1749. Phyllosphere environment of rice plant is usually inhabited by diverse bacteria which mostlycontribute beneficial effects to the plant fitness. TRFLP method is a rapid and straightforward method to determine the bacterialdiversity of many environments, including rice phyllosphere environment. This study aimed to analyze rice phyllosphere bacterialdiversity of healthy rice plant cultivar Ciherang obtained from Sukabumi, Jasinga, and Situgede. The bacterial genomes were amplifiedand digested with two restriction enzymes, i.e., MspI and BstUI. The bacterial diversity (H’ index) and evenness (E index) werecalculated from the peak value. From TRFs analysis, Betaproteobacteria and Pseudomonadales were dominantly found in nearly allsamples with different relative abundance. In addition, Alphaproteobacteria and Gammaproteobacteria were also dominant in the severalsamples. The unique bacteria groups were inhabited in the sample from specific regions with certain growth phase. This finding informsus that the geographical factors might be more influent than the growth phase factor. Furthermore, the bacterial diversity and evennessof the metagenomic approach are higher than cultivation-dependent approach.

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Shifts in the Oral Microbiota During a Four-Week Commercial Saturation Dive to 200 Meters

Frontiers in Physiology ◽

10.3389/fphys.2021.669355 ◽

2021 ◽

Vol 12 ◽

Author(s):

Roxane Monnoyer ◽

Kjersti Haugum ◽

Jacky Lautridou ◽

Arnar Flatberg ◽

Astrid Hjelde ◽

...

Keyword(s):

Bacterial Diversity ◽

Well Being ◽

Oral Microbiota ◽

Obligate Anaerobe ◽

Bacterial Composition ◽

Bacterial Phyla ◽

Transient Nature ◽

Hyperbaric Stress ◽

Bacterial Content ◽

Metagenomic Approach

During commercial saturation diving, divers live and work under hyperbaric and hyperoxic conditions. The myriads of bacteria that live in and on the human body must adjust to the resultant hyperbaric stress. In this study, we examined the shifts in bacterial content in the oral cavity of saturation divers, using a metagenomic approach to determine the diversity in the composition of bacterial phyla and genera in saliva from 23 male divers before, during, and immediately after 4 weeks of commercial heliox saturation diving to a working depth of circa 200 m. We found that the bacterial diversity fell during saturation, and there was a change in bacterial composition; with a decrease at the phylum level of obligate anaerobe Fusobacteria, and an increase of the relative abundance of Actinobacteria and Proteobacteria. At the genus level, Fusobacterium, Leptotrichia, Oribacterium, and Veillonella decreased, whereas Neisseria and Rothia increased. However, at the end of the decompression, both the diversity and composition of the microbiota returned to pre-dive values. The results indicate that the hyperoxic conditions during saturation may suppress the activity of anaerobes, leaving a niche for other bacteria to fill. The transient nature of the change could imply that hyperbaric heliox saturation has no lasting effect on the oral microbiota, but it is unknown whether or how a shift in oral bacterial diversity and abundance during saturation might impact the divers’ health or well-being.

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Bacterial diversity of smoked and smoked‐dried fish from West Africa: a metagenomic approach

Journal of Food Processing and Preservation ◽

10.1111/jfpp.15919 ◽

2021 ◽

Author(s):

Dona Gildas Hippolyte Anihouvi ◽

Olivier Henriet ◽

Yénoukounmè Euloge Kpoclou ◽

Marie‐Louise Scippo ◽

Djidjoho Joseph Hounhouigan ◽

...

Keyword(s):

West Africa ◽

Bacterial Diversity ◽

Dried Fish ◽

Metagenomic Approach

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Characterization of Biological Aerosols Over Northeast India: A Metagenomic Approach

10.21203/rs.3.rs-1081395/v1 ◽

2021 ◽

Author(s):

Binita Pathak ◽

Ankita Khataniar ◽

Barlin Das ◽

Sristisri Upadhyaya ◽

Ankita Medhi ◽

...

Keyword(s):

Bacterial Diversity ◽

Monsoon Season ◽

Fungal Spores ◽

Northeast India ◽

Microbial Biodiversity ◽

Operational Taxonomic Units ◽

Biological Aerosols ◽

Four Seasons ◽

Metagenomic Approach

Abstract Northeast India is considered as one of the major biodiversity hotspots in the world but the region is underexplored for their microbial biodiversity. Extensive characterization of biological aerosol (bioaerosol) samples collected from various locations of Northeast India was carried out for all the four seasons in a year. These were characterized in terms of particulate matters (inhalable, thoracic, and alveolic), their constituents (pollens, fungal spores, animal debris, and non-biological components), and finally the bacterial diversity was determined by DNA based metagenomic approach. The non-biological (non-viable) component of aerosols is found to vary from 30- 89% in pre-monsoon season which coexists with pollens (4-20%), animal debris (1-24%) and fungal spores (1-17%). The highest number of culturable microbial population in terms of CFU count was observed in the samples collected in pre-monsoon season (i.e., 125.24-632.45 CFU/m3) and the lowest CFU was observed in monsoon season (i.e., 20.83- 319.0 CFU/m3). The metagenomic approach with the samples collected during pre-monsoon season showed a total of bacterial 184 OTUs (operational taxonomic units) with 28,028 abundance count comprising with 7 major phylum, 6 classes, 10 orders, 15 families, 13 genus, and 8 species of bacteria. The species level distribution clearly shows the presence of Gammaproteobacteria (52%) most abundantly followed by Bacilli (21%), Alphaproteobacteria (14%), Betaproteobacteria (5%, Flavobacteria (5%), and Sphingobacteria (3%). It is the first report from entire Northeast India to uncover bacterial diversity in aerosol samples through DNA based metagenomic approach.

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16S rDNA-based bacterial diversity analysis of Arabian Sea sediments: A metagenomic approach

Ecological Genetics and Genomics ◽

10.1016/j.egg.2017.09.001 ◽

2017 ◽

Vol 3-5 ◽

pp. 47-51 ◽

Cited By ~ 2

Author(s):

Harisree P. Nair ◽

Rinu M. Puthusseri ◽

Helvin Vincent ◽

Sarita G. Bhat

Keyword(s):

Bacterial Diversity ◽

16S Rdna ◽

Arabian Sea ◽

Diversity Analysis ◽

Metagenomic Approach

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Bacterial diversity and abundance in shell biofilms from the freshwater snail Pleurocera canaliculatum (cerithioidea: Pleuroceridae)

Polish Journal of Microbiology ◽

10.33073/pjm-2015-027 ◽

2015 ◽

Vol 64 (2) ◽

pp. 181-184

Author(s):

RUSSELL L. MINTON ◽

CLINTON C. CREECH ◽

DEBRA W. JACKSON

Keyword(s):

Microbial Diversity ◽

Bacterial Diversity ◽

Freshwater Snail ◽

Hard Substrate ◽

Mollusk Shells ◽

Genus Level ◽

Metagenomic Approach ◽

Bivalve Shells

Mollusk shells provide a hard substrate for aquatic biofilm colonization. While most work has focused on bivalve shells and grazing, little work has focused on gastropod shells and the microbes growing on them. We sampled biofilms from 14 Pleuroceracanaliculatum and analyzed them using a metagenomic approach. Microbial diversity varied between individuals, and rarefaction suggested that 63 snails would need to be sampled to capture all of the estimated genus-level diversity. Cyanobacteria and species of Novosphingobium and Methylosoma were the most abundant taxa across all shells.

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