Construction &amp; assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data

Agnihotry, Shikha; Sarangi, Aditya Narayan; Aggarwal, Rakesh

doi:10.4103/ijmr.ijmr_220_18

Cited by 11 publications

(5 citation statements)

References 24 publications

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“…An important factor that only recently has gained attention is the importance of including absolute counts, e.g., by applying spike-in standards [ 76 ] or flow cytometry based cell counting [ 77 ], to overcome the limitations of working with relative abundances. Additionally, some attempts have been made to unify several reference databases containing sequences of 16S rRNA genes to improve taxonomic classification [ 78 ]. Other factors that may contribute to discrepant findings are differences in the number and recruitment process of participants, which might preclude the observation of small differences between groups, as well as lack of adjustment for relevant lifestyle-associated factors that have an influence in the composition and diversity of the gut microbiome [ 27 , 61 ].…”

Section: Discussionmentioning

confidence: 99%

Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis

et al. 2021

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Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing the gut microbiome composition by high-throughput sequencing in obese and non-obese adults. A significantly lower alpha diversity (Shannon index) in obese versus non-obese adults was observed in nine out of 22 studies, and meta-analysis of seven studies revealed a non-significant mean difference (−0.06, 95% CI −0.24, 0.12, I2 = 81%). At the phylum level, significantly more Firmicutes and fewer Bacteroidetes in obese versus non-obese adults were observed in six out of seventeen, and in four out of eighteen studies, respectively. Meta-analyses of six studies revealed significantly higher Firmicutes (5.50, 95% 0.27, 10.73, I2 = 81%) and non-significantly lower Bacteroidetes (−4.79, 95% CI −10.77, 1.20, I2 = 86%). At the genus level, lower relative proportions of Bifidobacterium and Eggerthella and higher Acidaminococcus, Anaerococcus, Catenibacterium, Dialister, Dorea, Escherichia-Shigella, Eubacterium, Fusobacterium, Megasphera, Prevotella, Roseburia, Streptococcus, and Sutterella were found in obese versus non-obese adults. Although a proportion of studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers.

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Section: Discussionmentioning

confidence: 99%

Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis

et al. 2021

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“…Representative ASVs were aligned with MAFFT and used for phylogenetic reconstruction in FastTree using plugin alignment and phylogeny ( Faith and Baker, 2006 ). A trained Naïve Bayes classifier-based SILVA database ( https://www.arb-silva.de/documentation/release-132/ ) was applied to assign the taxonomy ( Agnihortry et al, 2020 ; Kõljalg et al., 2020 ). ASVs that could not be taxonomically identified were manually checked by performing BLAST searches in RDP ( http://rdp.cme.msu.edu/ ) ( Bacci et al, 2015 ) based on similarity thresholds for family, genus, and species at >90, >95, and >97%, respectively ( Rosselló-Móra et al, 2017 ).…”

Section: Methodsmentioning

confidence: 99%

Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents

De-la-Vega-Camarillo,

Hernández-García,

Villa-Tanaca

et al. 2023

Front. Plant Sci.

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The bacterial component of plant holobiont maintains valuable interactions that contribute to plants’ growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.

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“…A recent strategy, called JTax, was proposed by Liu et al [ 57 ] based on joining non-overlapping reads and rearranging the reference sequences through primer sites accordingly. JTax was then used to join the filtered paired FASTQ files and to rebuild 16S-Udb, a reference unified database obtained by merging non-ambiguous, fully annotated, full-length 16S rRNA sequences from Greengenes, SILVA and Ribosomal Database Project (RDP) databases [ 58 ].…”

Section: Methodsmentioning

confidence: 99%

16S rRNA of Mucosal Colon Microbiome and CCL2 Circulating Levels Are Potential Biomarkers in Colorectal Cancer

Nardelli

Granata

Nunziato

et al. 2021

IJMS

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Colorectal cancer (CRC) is one of the most common malignancies in the Western world and intestinal dysbiosis might contribute to its pathogenesis. The mucosal colon microbiome and C-C motif chemokine 2 (CCL2) were investigated in 20 healthy controls (HC) and 20 CRC patients using 16S rRNA sequencing and immunoluminescent assay, respectively. A total of 10 HC subjects were classified as overweight/obese (OW/OB_HC) and 10 subjects were normal weight (NW_HC); 15 CRC patients were classified as OW/OB_CRC and 5 patients were NW_CRC. Results: Fusobacterium nucleatum and Escherichia coli were more abundant in OW/OB_HC than in NW_HC microbiomes. Globally, Streptococcus intermedius, Gemella haemolysans, Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were significantly increased in CRC patient tumor/lesioned tissue (CRC_LT) and CRC patient unlesioned tissue (CRC_ULT) microbiomes compared to HC microbiomes. CCL2 circulating levels were associated with tumor presence and with the abundance of Fusobacterium nucleatum, Bacteroides fragilis and Gemella haemolysans. Our data suggest that mucosal colon dysbiosis might contribute to CRC pathogenesis by inducing inflammation. Notably, Fusobacterium nucleatum, which was more abundant in the OW/OB_HC than in the NW_HC microbiomes, might represent a putative link between obesity and increased CRC risk.

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Construction & assessment of a unified curated reference database for improving the taxonomic classification of bacteria using 16S rRNA sequence data

Cited by 11 publications

References 24 publications

Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis

Gut Microbiome Composition in Obese and Non-Obese Persons: A Systematic Review and Meta-Analysis

Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents

16S rRNA of Mucosal Colon Microbiome and CCL2 Circulating Levels Are Potential Biomarkers in Colorectal Cancer

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