Microbiomics: An Approach to Community Microbiology

Sharma, Pankaj; Brahma, Vijaya; Sharma, Anamika; Dubey, Rama Kant; Sidhu, G. S.; Malhotra, Pawan Kumar

doi:10.1007/978-81-322-2172-2_22

Cited by 2 publications

(1 citation statement)

References 136 publications

(119 reference statements)

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“…Microbiomic analyses can give a microbial profile and the composition of a certain microbiome based on 16S ribosomal RNA sequences. Besides this, it can also provide a characterisation of community structure (Sharma et al 2015).…”

Section: ; Ashton Et Al 2014)mentioning

confidence: 99%

Scientific Report of Pediatric Irritable Bowel Disease Stool Samples Using MicrobiomeAnalyst

2022

JCMP

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Inflammatory bowel disease (IBD) is a disease with symptoms including weight loss, abdominal pain, bloody stools and persistent diarrhoea. According to current research, gut microbiota is considered to play an important role in IBD development. This analysis is of collected faecal samples from 43 children with IBD, specifically Crohn's disease (CD). MicrobiomeAnalyst software employing 16S rRNA sequencing was used to analyse the gut microbiota composition in the IBD patients, as well to enable comparison between the patients and a healthy control group. The analysis revealed that phylum Proteobacteria in the CD faecal samples was significantly higher than in the control, and also showed that abundance of genus Escherichia, species Coli and species Fragilis were also higher than in the control group without CD. This suggested that gut microbiota disorders are associated with intestinal inflammation. And while phylum Verrucomicrobia was present in the control group, it was apparently absent from the CD group. It was further found that Pseudomonas was positively correlated with Escherichia, while Faecalibacterium and Bacteroides were negatively correlated withEscherichia in the CD individuals. In addition, the diversity of gut microbiota among the individuals with CD was lower than for those without CD. It can be concluded that the disorder and the decrease in diversity of gut microbiota are related to intestinal inflammation, and specific relevant intestinal microbes are also evident.

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Section: ; Ashton Et Al 2014)mentioning

confidence: 99%

Scientific Report of Pediatric Irritable Bowel Disease Stool Samples Using MicrobiomeAnalyst

2022

JCMP

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Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota

Xiao

et al. 2018

Curr Microbiol

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The 16S rRNA gene is one of the most commonly used molecular markers for estimating bacterial diversity during the past decades. However, there is no consistency about the sequencing depth (from thousand to millions of sequences per sample), and the clustering methods used to generate OTUs may also be different among studies. These inconsistent premises make effective comparisons among studies difficult or unreliable. This study aims to examine the necessary sequencing depth and clustering method that would be needed to ensure a stable diversity patterns for studying fish gut microbiota. A total number of 42 samples dataset of Siniperca chuatsi (carnivorous fish) gut microbiota were used to test how the sequencing depth and clustering may affect the alpha and beta diversity patterns of fish intestinal microbiota. Interestingly, we found that the sequencing depth (resampling 1000-11,000 per sample) and the clustering methods (UPARSE and UCLUST) did not bias the estimates of the diversity patterns during the fish development from larva to adult. Although we should acknowledge that a suitable sequencing depth may differ case by case, our finding indicates that a shallow sequencing such as 1000 sequences per sample may be also enough to reflect the general diversity patterns of fish gut microbiota. However, we have shown in the present study that strict pre-processing of the original sequences is required to ensure reliable results. This study provides evidences to help making a strong scientific choice of the sequencing depth and clustering method for future studies on fish gut microbiota patterns, but at the same time reducing as much as possible the costs related to the analysis.

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Microbiomics: An Approach to Community Microbiology

Cited by 2 publications

References 136 publications

Scientific Report of Pediatric Irritable Bowel Disease Stool Samples Using MicrobiomeAnalyst

Scientific Report of Pediatric Irritable Bowel Disease Stool Samples Using MicrobiomeAnalyst

Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota

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