High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

ABSTRACT16S rRNA amplicon libraries from a haloarchaeal bloom in the hypersaline Dead Sea in 1992 were analyzed together with the 2007 residual population and simulated blooms in experimental mesocosms. Significant population shifts were observed during the bloom, and surprisingly a signature from the bloom was retained 15 years later.

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High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses

Applied and Environmental Microbiology ◽

10.1128/aem.00918-12 ◽

2012 ◽

Vol 78 (16) ◽

pp. 5717-5723 ◽

Cited By ~ 150

Author(s):

Lisa Quigley ◽

Orla O'Sullivan ◽

Tom P. Beresford ◽

R. Paul Ross ◽

Gerald F. Fitzgerald ◽

...

Keyword(s):

High Throughput ◽

Significant Influence ◽

High Throughput Sequencing ◽

Microbial Populations ◽

Bacterial Populations ◽

Content Type ◽

Pasteurized Milk ◽

First Time

ABSTRACTHere, high-throughput sequencing was employed to reveal the highly diverse bacterial populations present in 62 Irish artisanal cheeses and, in some cases, associated cheese rinds. Using this approach, we revealed the presence of several genera not previously associated with cheese, includingFaecalibacterium,Prevotella, andHelcococcusand, for the first time, detected the presence ofArthrobacterandBrachybacteriumin goats' milk cheese. Our analysis confirmed many previously observed patterns, such as the dominance of typical cheese bacteria, the fact that the microbiota of raw and pasteurized milk cheeses differ, and that the level of cheese maturation has a significant influence onLactobacilluspopulations. It was also noted that cheeses containing adjunct ingredients had lower proportions ofLactococcusspecies. It is thus apparent that high-throughput sequencing-based investigations can provide valuable insights into the microbial populations of artisanal foods.

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METAGENOMIC ANALYSIS TO IDENTIFY THE CAUSATIVE AGENTS OF ATYPICAL UROGENITAL TRACT INFECTIONS

Russian Journal of Infection and Immunity ◽

10.15789/2220-7619-mat-1713 ◽

2021 ◽

Author(s):

D. Kutilin

Keyword(s):

Chronic Inflammation ◽

High Throughput ◽

High Throughput Sequencing ◽

Urogenital Tract ◽

Metagenomic Analysis ◽

Healthy Individuals ◽

Microbiological Methods ◽

Wide Range ◽

Tract Infections ◽

Apparently Healthy

Importance. Research in recent decades has shown that classical microbiological methods can only detect a small, cultivable portion of microorganisms. One of the modern approaches to detect a wide range of bacteria and archaea is presented as a type of metagenomic analysis performed by high-throughput sequencing of ribosomal operon fragment libraries.Objective. Metagenomic analysis of samples from the urogenital tract of patients with chronic inflammation to identify pathogens not detected by other methods.Methods. Taxonomic analysis of the bacterial community was performed by high-throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene by using the Illumina HiSeq 3000 platform.Results. The study allowed to identify the taxonomic diversity of microorganisms in samples from the urogenital tract (from 197 to 794 different microorganisms belonging to the Bacteria were identified), as well as to establish differential differences concerning members of the genera Megasphaera, Prevotella, Veillonella, Pedobacter, Mobiluncus, Phobormidium, Sphing Temperatibacter, Oxobacter, Georgenia, Actinobaculum, Varibaculum, Mycobacterium, Rhodococcus, Sediminihabitans, Actinobacter, Actinoplanes, Spirochaeta, Enhydrobacter, Thermacetogenium, Bdellovibrio, Oleibacter, Porphyrom, Klebsiella, Lachnoclostridium, Caulobacter, Xanthomonas, Novispirillum, Marvinbryantia, afipia, Shinella, Tepidimonas, Faecalibacterium, Paludibacterium, Aerococcus, Campylobacter, Pasteurella, Rumen, Psychrobacter, Haemophilus, Brevibacillus, Sporosarcina, Yaniella and Lactobacillus between samples from patients with chronic inflammation and apparently healthy individuals.Conclusion. Differential differences were found in the composition of the microbiome from the samples of patients with chronic inflammation and apparently healthy individuals, concerning members of 44 genera, including Megasphaera, Prevotella, Veillonella, Pedobacter, Mobiluncus, Phormidium and Lactobacillus. The inflammatory processes observed in the patient urogenital tract can be associated with imbalanced microflora such as decreased level of typical members of the genera Staphylococcus, Streptococcus and Lactobacillus, but increased number of members from of the genera Klebsiella and Citrobacter.

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