Bacteria associated with human saliva are major microbial components of Ecuadorian indigenous beers (chicha)

Bacteria associated to human saliva are major microbial components of Ecuadorian indigenous beers (chicha)

10.7287/peerj.preprints.1520 ◽

2016 ◽

Cited By ~ 1

Author(s):

Ana L. Freire ◽

Sonia Zapata ◽

Juan Mosquera ◽

Maria Lorena Mejia ◽

Gabriel Trueba

Keyword(s):

Fermentation Process ◽

Bacterial Culture ◽

Human Saliva ◽

Oral Microbiota ◽

Indigenous Culture ◽

Streptococcus Salivarius ◽

Human Microbiota ◽

Amplicon Pyrosequencing

Indigenous beers (chicha) are part of the indigenous culture in Ecuador. The fermentation process of these beers relay probably on microorganisms from: fermenting substrates, environment and human microbiota. We analyzed the microbiota of artisanal beers (including a type of beer produced after chewing boiled cassava) using bacterial culture and 16S-based tag-encoded FLX amplicon pyrosequencing (bTEFAP). Surprisingly, we found that Streptococcus salivarius and Streptococcus mutans (part of the human oral microbiota) where among the most abundant bacteria in chewed cassava and in non-chewed cassava beers. We also demonstrated that S. salivarius and S. mutans (isolated from these beers) could proliferate in cassava mush. Lactobacillus sp. was predominantly present in most types of Ecuadorian chicha.

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Bacteria associated to human saliva are major microbial components of Ecuadorian indigenous beers (chicha)

10.7287/peerj.preprints.1520v2 ◽

2016 ◽

Cited By ~ 1

Author(s):

Ana L. Freire ◽

Sonia Zapata ◽

Juan Mosquera ◽

Maria Lorena Mejia ◽

Gabriel Trueba

Keyword(s):

Fermentation Process ◽

Bacterial Culture ◽

Human Saliva ◽

Oral Microbiota ◽

Indigenous Culture ◽

Streptococcus Salivarius ◽

Human Microbiota ◽

Amplicon Pyrosequencing

Indigenous beers (chicha) are part of the indigenous culture in Ecuador. The fermentation process of these beers relay probably on microorganisms from: fermenting substrates, environment and human microbiota. We analyzed the microbiota of artisanal beers (including a type of beer produced after chewing boiled cassava) using bacterial culture and 16S-based tag-encoded FLX amplicon pyrosequencing (bTEFAP). Surprisingly, we found that Streptococcus salivarius and Streptococcus mutans (part of the human oral microbiota) where among the most abundant bacteria in chewed cassava and in non-chewed cassava beers. We also demonstrated that S. salivarius and S. mutans (isolated from these beers) could proliferate in cassava mush. Lactobacillus sp. was predominantly present in most types of Ecuadorian chicha.

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Bacteria associated to human saliva are major microbial components of Ecuadorian indigenous beers (chicha)

10.7287/peerj.preprints.1520v1 ◽

2015 ◽

Author(s):

Ana L. Freire ◽

Sonia Zapata ◽

Juan Mosquera ◽

Gabriel Trueba

Keyword(s):

Fermentation Process ◽

Bacterial Culture ◽

Human Saliva ◽

Oral Microbiota ◽

Indigenous Culture ◽

Streptococcus Salivarius ◽

Human Microbiota ◽

Amplicon Pyrosequencing

Indigenous beers (chicha) are part of the indigenous culture in Ecuador. The fermentation process of these beers relay probably on microorganisms from: fermenting substrates, environment and human microbiota. We analyzed the microbiota of artisanal beers (including a type of beer produced after chewing boiled cassava) using bacterial culture and 16S-based tag-encoded FLX amplicon pyrosequencing (bTEFAP). Surprisingly, we found that Streptococcus salivarius and Streptococcus mutans (part of the human oral microbiota) where among the most abundant bacteria in chewed cassava and in non-chewed cassava beers. We also demonstrated that S. salivarius and S. mutans (isolated from these beers) could proliferate in cassava mush. Lactobacillus sp. was predominantly present in most types of Ecuadorian chicha.

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Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

10.21203/rs.3.rs-24857/v3 ◽

2020 ◽

Author(s):

Abigail Hui En Chan ◽

Kittipong Chaisiri ◽

Serge Morand ◽

Naowarat Saralamba ◽

Urusa Thaenkham

Keyword(s):

Genetic Marker ◽

Genetic Markers ◽

Molecular Systematics ◽

Ribosomal Rna ◽

Ribosomal Rna Genes ◽

16S Ribosomal Rna ◽

12S Rrna ◽

Rrna Gene ◽

12S Rrna Gene ◽

Rna Genes

Abstract Background Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics. Methods To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms. Results The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers. Conclusions This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

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Utility of Histologic and Histochemical Screening for 16S Ribosomal RNA Gene Sequencing of Formalin-Fixed, Paraffin-Embedded Tissue for Bacterial Endocarditis

American Journal of Clinical Pathology ◽

10.1093/ajcp/aqz055 ◽

2019 ◽

Vol 152 (4) ◽

pp. 431-437 ◽

Cited By ~ 1

Author(s):

Isaac H Solomon ◽

Chieyu Lin ◽

Katharine L Horback ◽

Sanjat Kanjilal ◽

Vanesa Rojas-Rudilla ◽

...

Keyword(s):

Ribosomal Rna ◽

Gene Sequencing ◽

Cost Savings ◽

16S Rrna Gene Sequencing ◽

16S Ribosomal Rna ◽

Molecular Testing ◽

Rrna Gene ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Formalin Fixed

Abstract Objectives 16S ribosomal RNA (rRNA) sequencing is a powerful but expensive tool for the identification of bacteria in culture-negative endocarditis. Histologic criteria to screen formalin-fixed, paraffin-embedded (FFPE) specimens for testing are evaluated. Methods Sixty-eight cases of infective endocarditis and controls were histologically reviewed and analyzed by 16S rRNA gene sequencing. Results Sequencing identified a specific pathogenic organism in 33 (49%) of 68 cases with acute inflammation and in 0 of 10 controls (P = .004). Visualization of organisms by Gram or Grocott methenamine silver stains had the strongest association with positive sequencing, while antibiotic treatment effect and acid decalcification decreased sensitivity. Molecular identifications were concordant with blood culture results in 90% of the cases, and a positive sequencing result was obtained in approximately half of the cases with negative valve cultures. Conclusions Histologic screening criteria are extremely helpful for identifying cases likely to be positive by molecular testing and can provide significant cost savings in filtering out low-yield specimens.

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Heterogeneity between 16S ribosomal RNA gene copies borne by one Desulfitobacterium strain is caused by different 100-200 bp insertions in the 5´ region

Canadian Journal of Microbiology ◽

10.1139/w06-111 ◽

2007 ◽

Vol 53 (1) ◽

pp. 116-128 ◽

Cited By ~ 13

Author(s):

Richard Villemur ◽

Philippe Constant ◽

Annie Gauthier ◽

Martine Shareck ◽

Réjean Beaudet

Keyword(s):

In Situ Hybridization ◽

16S Rrna ◽

16S Rrna Gene ◽

Ribosomal Rna ◽

16S Ribosomal Rna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Gene Copies

Strains of Desulfitobacterium hafniense, such as strains PCP-1, DP7, TCE1, and TCP-A, have unusual long 16S ribosomal RNA (rRNA) genes due to an insertion of approximately 100 bp in the 5' region. In this report, we analyzed the 16S rRNA genes of different Desulfitobacterium strains to determine if such an insertion is a common feature of desulfitobacteria. We amplified this region by polymerase chain reaction (PCR) from eight Desulfitobacterium strains (D. hafniense strains PCP-1, DP7, TCP-A, TCE1, and DCB-2; D. dehalogenans; D. chlororespirans; and Desulfitobacterium sp. PCE1) and resolved each PCR product by denaturing gradient gel electrophoresis (DGGE). All strains had from two to seven DGGE- migrating bands, suggesting heterogeneity in their 16S rRNA gene copies. For each strain, the 5' region of the 16S rRNA genes was amplified and a clone library was derived. Clones corresponding to most PCR–DGGE migration bands were isolated. Sequencing of representative clones revealed that the heterogeneity was generated by insertions of 100–200 bp. An insertion was found in at least one copy of the 16S rRNA gene in all examined strains. In total, we found eight different types of insertions (INS1–INS8) that varied from 123 to 193 nt in length. Two-dimensional structural analyses of transcribed sequences predicted that all insertions would form an energetically stable loop. Reverse transcriptase – PCR experiments revealed that most of the observed insertions in the Desulfitobacterium strains were excised from the mature 16S rRNA transcripts. Insertions were not commonly found in bacterial 16S rRNA genes, and having a different insertion in several 16S rRNA gene copies borne by a single bacterial species was rarely observed. The function of these insertions is not known, but their occurrence can have an important impact in deriving 16S rRNA oligonucleotidic fluorescence in situ hybridization probes, as these insertions can be excised from 16S rRNA transcripts.Key words: Desulfitobacterium, 16S ribosomal RNA genes, heterogeneity, gene insertions, fluorescence in situ hybridization.

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Correlation of rRNA gene amplicon pyrosequencing and bacterial culture for microbial compositional analysis of faecal samples from elderly Irish subjects

Journal of Applied Microbiology ◽

10.1111/j.1365-2672.2011.05067.x ◽

2011 ◽

Vol 111 (2) ◽

pp. 467-473 ◽

Cited By ~ 17

Author(s):

Ó. O’Sullivan ◽

M. Coakley ◽

B. Lakshminarayanan ◽

M.J. Claesson ◽

C. Stanton ◽

...

Keyword(s):

Bacterial Culture ◽

Compositional Analysis ◽

Rrna Gene ◽

Amplicon Pyrosequencing ◽

Faecal Samples

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Evaluation and utility of mitochondrial ribosomal genes for molecular systematics of parasitic nematodes

10.21203/rs.3.rs-24857/v1 ◽

2020 ◽

Author(s):

Abigail Hui En Chan ◽

Kittipong Chaisiri ◽

Serge Morand ◽

Naowarat Saralamba ◽

Urusa Thaenkham

Keyword(s):

Genetic Marker ◽

Genetic Markers ◽

Molecular Systematics ◽

Ribosomal Rna ◽

Ribosomal Rna Genes ◽

16S Ribosomal Rna ◽

12S Rrna ◽

Rrna Gene ◽

12S Rrna Gene ◽

Rna Genes

Abstract Background: Molecular advances have accelerated our understanding of nematode systematics and taxonomy. However, comparative analyzes between various genetic markers have led to discrepancies in nematode phylogenies. This study aimed to evaluate the suitability of using mitochondrial 12S and 16S ribosomal RNA genes for nematode molecular systematics.Methods: To study the suitability of mitochondrial 12S and 16S ribosomal RNA genes as genetic markers for nematode molecular systematics, we compared them with the other commonly used genetic markers, nuclear internal transcribed spacer 1 and 2 regions, nuclear 18S and 28S ribosomal RNA genes, and mitochondrial cytochrome c oxidase subunit 1 gene. After that, phylum-wide primers for mitochondrial 12S and 16S ribosomal RNA genes were designed, and parasitic nematodes of humans and animals from 75 taxa with 21 representative species were inferred through phylogenetic analyzes. Phylogenetic analyzes were carried out using maximum likelihood and Bayesian inference algorithms. Results: The phylogenetic relationships of nematodes based on the mitochondrial 12S rRNA gene supported the monophyly of nematodes in clades I, IV, and V, reinforcing the potential of this gene as a genetic marker for nematode systematics. In contrast, the mitochondrial 16S rRNA gene only supported the monophyly of clades I and V, providing evidence that the 12S rRNA gene is more suitable for nematode molecular systematics. In this study, subclades of clade III containing various nematode families were not monophyletic when the 16S or 12S rRNA gene was used as the genetic marker. This is similar to the phylogenetic relationship revealed by previous studies using whole mitochondrial genomes as genetic markers. Conclusions: This study supports the use of the 12S rRNA gene as a genetic marker for studying the molecular systematics of nematodes to understand intra-phyla relationships. Phylum-wide primers for nematodes using mitochondrial ribosomal genes were prepared, which may enhance future studies. Furthermore, sufficient genetic variation in the mitochondrial 12S and 16S rRNA genes between species also allowed for accurate taxonomy to species level, revealing the potential of these two genes as genetic markers for DNA barcoding.

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Endodontic Recontamination and Retreatment: The Concise Systematic Review

MedNEXT Journal of Medical and Health Sciences ◽

10.54448/mdnt2142 ◽

2021 ◽

Vol 2 (4) ◽

Author(s):

Beatriz De Oliveira Merotti ◽

Laura Souza De Morais ◽

Gestter Willian Lattari Tessarin

Keyword(s):

Literature Review ◽

Systematic Literature Review ◽

Ribosomal Rna ◽

Root Canal ◽

Gene Sequencing ◽

16S Ribosomal Rna ◽

Molecular Technique ◽

Rrna Gene ◽

Root Canals

Introduction: It is necessary to know the nature of the endodontic microbiota within the root canal system of teeth with necrotic pulp tissues. There are several methods of microbial identification, including techniques based on culture or non-predominance of facultative anaerobes and Gram-positive species, especially Enterococcus faecalis. The 16S ribosomal RNA (rRNA) gene sequencing approach has become the reference method. Polymerase chain reaction (PCR) is a molecular technique also used. A condition for successful endodontic retreatment is proper cleaning of the root canals. Objective: Evaluate through a systematic literature review the main contaminations, recontaminations, and endodontic retreatments in root canals. Methods: The present study was followed by a systematic literature review model, according to the PRISMA rules. Clinical studies included case reports, retrospective, prospective and randomized trials. The quality of the studies was based on the GRADE instrument. The risk of bias was analyzed according to the Cochrane instrument. Results: A total of 94 articles were found. A total of 58 articles were evaluated in full, and 34 were included and discussed in this study. The overall assessment did not result in significant risks that could compromise the science of the present study. According to the GRADE classification, the studies were of moderate quality. Conclusion: It was concluded that it is essential to characterize the microbiota of root canals with failed endodontic treatment through 16S ribosomal RNA (GS) gene sequencing and PCR. Furthermore, it can be stated that the root canal instrumentation system with rotating files maintains the quality of root preparation, reducing the operative time and also the risk of a torsional fracture within the root canal.

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Exploring the genetic diversity of the 16S rRNA gene of Akkermansia muciniphila in IBD and IBS

Future Microbiology ◽

10.2217/fmb-2019-0175 ◽

2019 ◽

Vol 14 (17) ◽

pp. 1497-1509 ◽

Cited By ~ 3

Author(s):

Alessandra Lo Presti ◽

Federica Del Chierico ◽

Annamaria Altomare ◽

Francesca Zorzi ◽

Eleonora Cella ◽

...

Keyword(s):

Genetic Diversity ◽

Ribosomal Rna ◽

Protective Role ◽

16S Ribosomal Rna ◽

Rrna Gene ◽

Rna Sequences ◽

Akkermansia Muciniphila ◽

Ribosomal Rna Sequences ◽

Bowel Diseases ◽

Inflammatory Bowel

Aim: The human gastrointestinal tract harbors diverse, abundant microbiota and Akkermansia muciniphila is involved in this community. The aim of this study is to characterize 16 new A. muciniphila 16S ribosomal RNA sequences selected from a metagenomic database from stools of patients with irritable bowel syndrome (IBS), inflammatory bowel diseases and control (CTRLs) subjects by a phylogenetic approach. Materials & methods: A phylogenetic approach was used to study the genetic diversity and SNPs in 16 A. muciniphila 16S ribosomal RNA sequences from stools of 107 individuals, 36 of which were patients affected by IBS, 30 by inflammatory bowel disease and 41 were CTRLs. Results: Phylogenetic analysis confirmed the subdivision into different supported clusters. An increase of variability in IBS has been identified. Conclusion: The genetic variation combined to the relative abundance, contribute to the protective role of A. muciniphila. Phylogenesis represent an additional approach to investigate genetic variability.

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