Full-length 16S rRNA gene sequencing combined with adequate database selection improves the description of Arctic marine prokaryotic communities DOI Creative Commons
Francisco Pascoal, Pedro Duarte, Philipp Assmy

et al.

Annals of Microbiology, Journal Year: 2024, Volume and Issue: 74(1)

Published: Aug. 10, 2024

Abstract Background High-throughput sequencing of the full-length 16S rRNA gene has improved taxonomic classification prokaryotes found in natural environments. However, shorter regions from same gene, like V4-V5 region, can provide more cost-effective high throughput. It is unclear which approach best describes prokaryotic communities underexplored In this study, we hypothesize that high-throughput combined with adequate databases improves description environments comparison a short region gene. Results To test our hypothesis, compared profiles seawater samples Arctic Ocean using: and combination either Genome Taxonomy Database (GTDB) or Silva taxonomy database. Our results show all combinations strategies present similar at higher levels. lower levels, namely family, genus, most notably species level, led to proportions Amplicon Sequence Variants (ASVs) assigned formally valid taxa. Hence, was obtained by GTDB combination, some cases allowed for identification intraspecific diversity ASVs. Conclusions We conclude coupling microbiome profiling ranks. The improvements reported here context scientists discuss microbial community dynamics within solid framework still underrepresented sequences public databases.

Language: Английский

Assembly mechanism of microbial community under different seasons in Shantou sea area DOI

Peng Zheng,

Aihua Mao,

Shanshan Meng

et al.

Marine Pollution Bulletin, Journal Year: 2024, Volume and Issue: 205, P. 116550 - 116550

Published: June 15, 2024

Language: Английский

Citations

6
Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization DOI Creative Commons
Jianshi Jin,

Xiongduo Liu,

Katsuyuki Shiroguchi

et al.

iMetaOmics., Journal Year: 2024, Volume and Issue: 1(1)

Published: July 11, 2024

Abstract Bacteria often exist and function as a community, known the bacterial microbiota, which consists of vast numbers bacteria belonging to many species (taxa). Characterizing microbiota needs high‐throughput approaches that enable identification quantification cells, such have been under development for more than 30 years. In this review, we describe history technologies based on 16S ribosomal RNA (rRNA) gene‐amplicon sequencing characterization microbiotas. Then, summarize features applications current rRNA approaches, including recent achievement enables individual cells with single‐base accuracy genes identified cells. Furthermore, present prospects further technical development, combined use methods other informative analyses, whole‐genome in common unit cell, both number their functions.

Language: Английский

Citations

6
Remarkable characteristics and distinct community of biofilms on the photoaged polyethylene films in riverine microcosms DOI

Hexinyue Huang,

Peng Liu,

Yanqi Shi

et al.

Environmental Pollution, Journal Year: 2021, Volume and Issue: 292, P. 118485 - 118485

Published: Nov. 10, 2021

Language: Английский

Citations

35
Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems DOI Creative Commons
Jessica Rieder, Adamandia Kapopoulou, Claudia Bank

et al.

Environmental Microbiome, Journal Year: 2023, Volume and Issue: 18(1)

Published: Feb. 14, 2023

Microbial communities in recirculating aquaculture systems (RAS) play a role system success, nutrient cycling, and water quality. Considering the increasing socio-economic of fish farming, e.g., regarding food security, an in-depth understanding microbial is also relevant from management perspective, especially growth, development, welfare farmed animal. However, current data on composition within RAS patchy, which partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there need for accurate, standardized, user-friendly methods study systems.We compared sequencing approach performances (3 types 16S short amplicon sequencing, PacBio long-read amplification-free shotgun metagenomics) characterization two commercial farms. Results showed primer choice length affect some values (e.g., diversity measures, number assigned taxa or distinguishing ASVs) but have no impact spatio-temporal patterns between sample types, farms time points. This implies rRNA approaches are adequate community studies. The amplicons underperformed quantitative resolution were suited identify functional services, nitrification cycling detection pathogens. Finally, metagenomics extended picture fungi, viruses, bacteriophages, opening avenues exploring inter-domain interactions. All datasets agreed major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, Proteobacteria.The different yielded overlapping highly complementary results, with each contributing unique not obtainable other approaches. We conclude tiered constitutes strategy obtaining maximum amount information can inform basic research evolution dynamics. For specific and/or applied questions, single-method more practical cost-effective could lead better farm practices.

Language: Английский

Citations

16
High-throughput DNA metabarcoding for determining the gut microbiome of captive critically endangered Malayan tiger (Panthera tigris jacksoni) during fasting DOI Creative Commons
Mohamad Khairulmunir, Millawati Gani, Kayal Vizi Karuppannan

et al.

Biodiversity Data Journal, Journal Year: 2023, Volume and Issue: 11

Published: Sept. 5, 2023

The Malayan tiger (Pantheratigrisjacksoni) is a critically endangered species native to the Malaysian Peninsula. To imitate wild conditions where tigers do not hunt every day, numerous wildlife sanctuaries feed their daily. However, effects of fasting on gut microbiota captive remains unknown. This study aimed characterise by comparing microbial communities during versus normal feeding conditions. was conducted at Melaka Zoo, Peninsula and involved fasted Monday. In total, ten faecal samples tiger, two Bengal (outgroup) four lion were collected analysed for metabarcoding targeting 16S rRNA V3-V4 region. we determined 14 phyla, 87 families, 167 genera 53 microbiome across samples. potentially harmful bacterial found in this included Fusobacterium, Bacteroides, Clostridium sensu stricto 1, Solobacterium, Echerichiashigella, Ignatzschineria Negativibacillus. phase had higher composition more diverse than phase. present findings indicate balanced ratio dominant reflecting resetting imbalanced due fasting. These can help authorities how best maintain improve husbandry health captivity be used monitoring ex-situ veterinary care unit.

Language: Английский

Citations

16
Influences of hydrodynamics on microbial community assembly and organic carbon composition of resuspended sediments in shallow marginal seas DOI
Yangli Che, Chaoran Lin, Shen Li

et al.

Water Research, Journal Year: 2023, Volume and Issue: 248, P. 120882 - 120882

Published: Nov. 15, 2023

Language: Английский

Citations

15
High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change DOI Creative Commons
Walaa K. Mousa, Tareq Abu‐Izneid, Ahmed Salah-Tantawy

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: March 5, 2024

Introduction Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, functions these communities imperative to navigate global changes confront potential threats opportunities applicable agricultural amid climate change. Methods This study explores in rhizosphere endosphere desert plants native Arabian Peninsula using next-generation sequencing 16S rRNA gene (V3-V4 hypervariable region). Results Our results reveal each community has diverse composition. Based on alpha beta indices, microbiome significantly richer taxa compared endosphere. The data reveals shift towards fast-growing microbes with active metabolism, involvement nutrient cycling, nitrogen fixation, defense pathways. presence habitat-specific desert, highlighting their remarkable resilience adaptability extreme environmental conditions. Notably, we observed existence radiation-resistant such as Deinococcus radiotolerans, Kocuria sp., Rubrobacter radiotolerans which can tolerate high levels ionizing radiation. Additionally, examples exhibiting tolerance challenging conditions include Nocardioides halotolerans, thriving high-salinity environments, hyperthermophilic Quasibacillus thermotolerans. Moreover, functional analysis enrichment chaperon biosynthesis pathways associated correct protein folding under heat stress Discussion research sheds light underscores applications increase agriculture ecosystems, offering promising strategy fortify crops against challenges posed by change, ultimately supporting sustainable food production our ever-expanding population.

Language: Английский

Citations

5
Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling DOI Creative Commons
Vitor Heidrich, Lilian T. Inoue, Paula Fontes Asprino

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2022, Volume and Issue: 12

Published: April 21, 2022

Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene is widely used for microbiota with NGS technologies. Since most platforms generate short reads, full-length rRNA impractical. Therefore, choosing which hypervariable region sequence critical studies. All nine regions are taxonomically informative, but due variability performance specific clades, ideal will depend on bacterial composition habitat under study. Recently, allowed identification microbes urinary tract, and become an active research area. However, there no current study evaluating different male profiling. We collected urine samples from volunteers profiled their by a panel six amplicons encompassing all regions. Systematic comparisons indicate V1V2 better assess taxa commonly present samples, suggesting amplicon more suitable believe our results be helpful guide this crucial methodological choice future

Language: Английский

Citations

21
16S rRNA gene primer choice impacts off-target amplification in human gastrointestinal tract biopsies and microbiome profiling DOI Creative Commons
Tereza Deissová, Martina Zapletalová, Lumír Kunovský

et al.

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Aug. 3, 2023

16S rRNA amplicon sequencing or, more recently, metatranscriptomic analysis are currently the only preferred methods for microbial profiling of samples containing a predominant ratio human to bacterial DNA. However, due off-target amplification DNA, current protocols inadequate bioptic samples. Here we present an efficient, reliable, and affordable method bacteriome clinical DNA content predominates. We determined microbiota profile in total 40 biopsies esophagus, stomach, duodenum using with widely used 515F-806R (V4) primers targeting V4 region, 68F-338R modified set (V1-V2M) V1-V2 region. With primers, on average 70% sequence variants (ASV) mapped genome. On other hand, this was absent when V1-V2M primers. Moreover, provided significantly higher taxonomic richness reproducibility compared conclude that is cost-effective, applicable low-bacterial abundant medical research.

Language: Английский

Citations

13
Gut microbiome profiling of neonates using Nanopore MinION and Illumina MiSeq sequencing DOI Creative Commons
Teahyen Cha, Hoo Hugo Kim, Jihyun Keum

et al.

Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14

Published: May 15, 2023

This study aimed to evaluate the difference in gut microbiomes between preterm and term infants using third-generation long-read sequencing (Oxford Nanopore Technologies, ONT) compared with an established gold standard, Illumina (second-generation short-read sequencing). A total of 69 fecal samples from 51 (T) (P) were collected at 7 28 days life. Gut colonization profiling was performed by 16S rRNA gene ONT. We used validate compare patterns 13 neonates. Using bioinformatic analysis, we identified features that differed P T. Both T1 P1 dominated Firmicutes (Staphylococcus Enterococcus), whereas sequentially showed dominant transitions Lactobacillus (p < 0.001) Streptococcus T2 = 0.001), pathogenic bacteria (Klebsiella) P2 0.001). The abundance beneficial (Bifidobacterium Lactobacillus) increased 0.026 p 0.001, respectively). These assignments correlated species-level. Bacterial α-diversity T 0.005) but not 0.156), distinct β-diversity clustering than ONT reliably genus level, taxonomic profiles comparable those level. shows are highly correlated. had different microbiome profiles, α- varied. has potential for pathogen detection neonates clinical settings.

Language: Английский

Citations

11