scholarly journals A Metagenomic-Based Approach for the Characterization of Bacterial Diversity Associated with Spontaneous Malolactic Fermentations in Wine

2019 ◽  
Vol 20 (16) ◽  
pp. 3980 ◽  
Author(s):  
Carmen Berbegal ◽  
Luigimaria Borruso ◽  
Mariagiovanna Fragasso ◽  
Maria Tufariello ◽  
Pasquale Russo ◽  
...  
Keyword(s):  
Malic Acid ◽  
Alcoholic Fermentation ◽  
Oenococcus Oeni ◽  
Taxonomic Composition ◽  
Starter Cultures ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Microbial Resources ◽  
Next Generation Sequencing Ngs ◽  
First Time

This study reports the first application of a next generation sequencing (NGS) analysis. The analysis was designed to monitor the effect of the management of microbial resources associated with alcoholic fermentation on spontaneous malolactic consortium. Together with the analysis of 16S rRNA genes from the metagenome, we monitored the principal parameters linked to MLF (e.g., malic and lactic acid concentration, pH). We encompass seven dissimilar concrete practices to manage microorganisms associated with alcoholic fermentation: Un-inoculated must (UM), pied-de-cuve (PdC), Saccharomyces cerevisiae (SC), S. cerevisiae and Torulaspora delbrueckii co-inoculated and sequentially inoculated, as well as S. cerevisiae and Metschnikowia pulcherrima co-inoculated and sequentially inoculated. Surprisingly, each experimental modes led to different taxonomic composition of the bacterial communities of the malolactic consortia, in terms of prokaryotic phyla and genera. Our findings indicated that, uncontrolled AF (UM, PdC) led to heterogeneous consortia associated with MLF (with a relevant presence of the genera Acetobacter and Gluconobacter), when compared with controlled AF (SC) (showing a clear dominance of the genus Oenococcus). Effectively, the SC trial malic acid was completely degraded in about two weeks after the end of AF, while, on the contrary, malic acid decarboxylation remained uncomplete after 7 weeks in the case of UM and PdC. In addition, for the first time, we demonstrated that both (i) the inoculation of different non-Saccharomyces (T. delbrueckii and M. pulcherrima) and, (ii) the inoculation time of the non-Saccharomyces with respect to S. cerevisiae resources (co-inoculated and sequentially inoculated) influence the composition of the connected MLF consortia, modulating MLF performance. Finally, we demonstrated the first findings of delayed and inhibited MLF when M. pulcherrima, and T. delbrueckii were inoculated, respectively. In addition, as a further control test, we also assessed the effect of the inoculation with Oenococcus oeni and Lactobacillus plantarum at the end of alcoholic fermentation, as MLF starter cultures. Our study suggests the potential interest in the application of NGS analysis, to monitor the effect of alcoholic fermentation on the spontaneous malolactic consortium, in relation to wine.

scholarly journals Sputum Microbiome Composition in Patients With Squamous Cell Lung Carcinoma

2021 ◽  
Author(s):  
E. D. Baranova ◽  
V. G. Druzhinin ◽  
L. V. Matskova ◽  
P. S. Demenkov ◽  
V. P . Volobaev ◽  
...  
Keyword(s):  
Squamous Cell ◽  
Inflammatory Responses ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Cell Lung Carcinoma ◽  
Microbiome Composition ◽  
Β Diversity ◽  
Genome Damage

Abstract Recent findings indicate that the microbiome can have a significant impact on the development of lung cancer by inducing inflammatory responses, causing dysbiosis and generating genome damage. The aim of this study was to search for bacterial markers of squamous cell carcinoma (LUSC). In the study, the taxonomic composition of the sputum microbiome of 40 men with untreated LUSC was compared with 40 healthy controls. Next Generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. There was no differences in alpha diversity between the LUSC and control groups. Meanwhile, differences in the structure of bacterial communities (β diversity) among patients and controls differed significantly in sputum samples (pseudo-F = 1.65; p = 0.026). Only Streptococcus, Bacillus, Gemella and Haemophilus were found to be significantly increased in patients with LUSC compared to the control subjects, while 19 bacterial genera were significantly reduced, indicating a decrease in beta diversity in the microbiome of patients with LUSC. From our study, Streptococcus (Streptococcus agalactiae) emerges as the most likely LUSC biomarker, but more research is needed to confirm this assumption.

scholarly journals Taxonomic composition and biodiversity of the gut microbiome from patients with irritable bowel syndrome, ulcerative colitis, and asthma

2022 ◽  
Vol 25 (8) ◽  
pp. 864-873
Author(s):  
A. Y. Tikunov ◽  
A. N. Shvalov ◽  
V. V. Morozov ◽  
I. V. Babkin ◽  
G. V. Seledtsova ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Irritable Bowel Syndrome ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Taxonomic Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Taxonomic Structure ◽  
Opportunistic Bacteria ◽  
Irritable Bowel

To date, the association of an imbalance of the intestinal microbiota with various human diseases, including both diseases of the gastrointestinal tract and disorders of the immune system, has been shown. However, despite the huge amount of accumulated data, many key questions still remain unanswered. Given limited data on the composition of the gut microbiota in patients with ulcerative colitis (UC) and irritable bowel syndrome (IBS) from different parts of Siberia, as well as the lack of data on the gut microbiota of patients with bronchial asthma (BA), the aim of the study was to assess the biodiversity of the gut microbiota of patients with IBS, UC and BA in comparison with those of healthy volunteers (HV). In this study, a comparative assessment of the biodiversity and taxonomic structure of gut microbiome was conducted based on the sequencing of 16S rRNA genes obtained from fecal samples of patients with IBS, UC, BA and volunteers. Sequences of the Firmicutes and Bacteroidetes types dominated in all samples studied. The third most common in all samples were sequences of the Proteobacteria type, which contains pathogenic and opportunistic bacteria. Sequences of the Actinobacteria type were, on average, the fourth most common. The results showed the presence of dysbiosis in the samples from patients compared to the sample from HVs. The ratio of Firmicutes/Bacteroidetes was lower in the IBS and UC samples than in HV and higher the BA samples. In the samples from patients with intestinal diseases (IBS and UC), an increase in the proportion of sequences of the Bacteroidetes type and a decrease in the proportion of sequences of the Clostridia class, as well as the Ruminococcaceae, but not Erysipelotrichaceae family, were found. The IBS, UC, and BA samples had signif icantly more Proteobacteria sequences, including Methylobacterium, Sphingomonas, Parasutterella, Halomonas, Vibrio, as well as Escherichia spp. and Shigella spp. In the gut microbiota of adults with BA, a decrease in the proportion of Roseburia, Lachnospira, Veillonella sequences was detected, but the share of Faecalibacterium and Lactobacillus sequences was the same as in healthy individuals. A signif icant increase in the proportion of Halomonas and Vibrio sequences in the gut microbiota in patients with BA has been described for the f irst time.

scholarly journals Investigating the microbiota of fermented fish products (Pla-ra) from different communities of northeastern Thailand

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245227
Author(s):  
Rutchanee Rodpai ◽  
Oranuch Sanpool ◽  
Tongjit Thanchomnang ◽  
Arporn Wangwiwatsin ◽  
Lakkhana Sadaow ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Raw Materials ◽  
Abundant Species ◽  
Industrial Applications ◽  
Bifidobacterium Bifidum ◽  
Starter Cultures ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Lactobacillus Pentosus ◽  
Northeastern Thailand

DNA-sequencing was performed on the V3-V4 regions of 16S rRNA genes to investigate the microbial diversity of five samples of fermented freshwater fish (pla-ra) from three provinces in northeastern Thailand. The samples had salt concentrations ranging from 7 to 10%, pH values from 4.83 to 7.15, and D-/L-lactic acid concentrations of 90 to 450 mg/l. A total of 598 operational taxonomic units were annotated at various taxonomic ranks based on the SILVA Database. The lactic-acid and halophilic genera Tetragenococcus, Halanaerobium and Lactobacillus were among the dominant taxa of bacteria. The top 20 non-redundant taxa were considered in more detail. In two pla-ra samples, Tetragenococcus muriaticus was commonly identified. Halanaerobium fermentans was the most abundant species in a third sample and co-dominant in another sample. Lactobacillus rennini was dominant in the pla-ra sample from Roi Et Province. Additionally, other beneficial bacteria were detected including Staphylococcus nepalensis, Lactobacillus sakei, Lactobacillus pentosus, Weissella confusa, and Bifidobacterium bifidum. Differences between samples may be due to use of different raw materials, salt concentrations, recipes, processes and fermentation periods. The microbial communities in pla-ra provide a better understanding of the production outcomes of traditional products. Further optimization of the fermentation process, for example by using dominant bacterial taxa in starter cultures, may improve processes of food fermentation, food quality and flavor control, providing useful guidelines for industrial applications.

scholarly journals Disturbance During Biofilm Community Succession Promotes Cooperation and Diversity

2018 ◽  
Author(s):  
James P. Stratford ◽  
Douglas M. Hodgson ◽  
Nelli J. Beecroft ◽  
Ann Smith ◽  
Julian R. Marchesi ◽  
...  
Keyword(s):  
Time Course ◽  
Explanatory Power ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Widespread Application ◽  
Operational Taxonomic Units ◽  
Microbial Biofilms ◽  
Macro Scale ◽  
First Time ◽  
High Diversity

AbstractDiversity-disturbance relationships have found widespread application in ecology, conservation and biodiversity management. In spite of their explanatory power, these conceptual frameworks have yet to be systematically applied to understanding succession in diverse microbial biofilms. Here we investigate community assembly in biofilms formed in replicate microbial bioelectrochemical systems using time-course sequencing of community 16S rRNA genes, corresponding to hundreds of operational taxonomic units (OTUs). For the first time we present a statistical model showing that a simple diversity-disturbance relationship can be used to explain dynamic changes in high diversity biofilm communities. This simple model reveals that succession in these systems is guided towards either a low diversity, generalist-dominated biofilm or a high diversity, cooperative-specialist biofilm, depending on the level of endogenous disturbance measured within the community. The pattern observed shows remarkable symmetry with findings from macro-scale communities such as grasslands, forests and coral reefs.

scholarly journals Characterization of Bioaerosols from Dairy Barns: Reconstructing the Puzzle of Occupational Respiratory Diseases by Using Molecular Approaches

2012 ◽  
Vol 78 (9) ◽  
pp. 3242-3248 ◽  
Author(s):  
Pascale Blais Lecours ◽  
Marc Veillette ◽  
David Marsolais ◽  
Caroline Duchaine
Keyword(s):  
16S Rrna ◽  
Respiratory Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Exact Nature ◽  
Continuous Exposure ◽  
Content Type ◽  
Humoral Immune ◽  
Molecular Approaches ◽  
First Time

ABSTRACTTo understand the etiology of exposure-related diseases and to establish standards for reducing the risks associated with working in contaminated environments, the exact nature of the bioaerosol components must be defined. Molecular biology tools were used to evaluate airborne bacterial and, for the first time, archaeal content of dairy barns. Three air samplers were tested in each of the 13 barns sampled. Up to 106archaeal and 108bacterial 16S rRNA genes per m3of air were detected. Archaeal methanogens, mainlyMethanobrevibacterspecies, were represented.Saccharopolyspora rectivirgula, the causative agent of farmer's lung, was quantified to up to 10716S rRNA genes per m3of air. In addition, a wide variety of bacterial agents were present in our air samples within the high airborne bioaerosol concentration range. Despite recommendations regarding hay preservation and baling conditions, farmers still develop anS. rectivirgula-specific humoral immune response, suggesting intense and continuous exposure. Our results demonstrate the complexity of bioaerosol components in dairy barns which could play a role in occupational respiratory diseases.

scholarly journals Effects of Gasterophilus pecorum infestation on the intestinal microbiota of the rewilded Przewalski’s horses in China

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251512
Author(s):  
Dini Hu ◽  
Yuzhu Chao ◽  
Boru Zhang ◽  
Chen Wang ◽  
Yingjie Qi ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
High Throughput Sequencing ◽  
Nature Reserve ◽  
Sequence Data ◽  
Parasitic Infection ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bioinformatics Analyses ◽  
Gasterophilus Pecorum ◽  
First Time

Horse botflies have been a threat to the Przewalski’s horses in the Kalamaili Nature Reserve in Xinjiang of China since their reintroduction to the original range. As larvae of these parasites could infest the intestine of a horse for months, they could interact with and alter the structure and composition of its intestinal microbiota, affecting adversely its health. Nonetheless, there are no such studies on the rewilded Przewalski’s horses yet. For the first time, this study characterizes the composition of the intestinal microbiota of 7 rewilded Przewalski’s horses infected severely by Gasterophilus pecorum following and prior to their anthelmintic treatment. Bioinformatics analyses of the sequence data obtained by amplicon high throughput sequencing of bacterial 16S rRNA genes showed that G. pecorum infestation significantly increased the richness of the intestinal microbial community but not its diversity. Firmicutes and Bacteroidetes were found the dominant phyla as in other animals, and the parasitic infestation decreased the F/B ratio largely by over 50%. Large reduction in relative abundances of the two genera Streptococcus and Lactobacillus observed with G. pecorum infestation suggested possible changes in colic and digestion related conditions of the infected horses. Variations on the relative abundance of the genus groups known to be pathogenic or symbiotic showed that adverse impact of the G. pecorum infestation could be associated with reduction of the symbiotic genera Lactobacillus and Bifidobacterium that are probiotics and able to promote immunity against parasitic infection.

Identification of Dominant Bacteria Isolated From Periodontal Abscesses

2021 ◽  
pp. 232020682110507
Author(s):  
Kubra Karacam ◽  
Turgut Demir ◽  
Ozlem Baris
Keyword(s):  
Bacterial Species ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rdna Sequencing ◽  
Bacterial Content ◽  
Dominant Bacteria ◽  
Research Criteria ◽  
First Time ◽  
Culture Dependent

Aim: Various methods investigating the bacterial content causing periodontal abscesses have been applied in studies conducted until today. However, these studies have focused on periodontopathogens. Our study was carried out to research whether different pathogens other than the known periodontopathogens are present in periodontal abscess formation. Therefore, dominant bacterial samples obtained from the periodontal abscess content using the culture-dependent method were identified by 16S rDNA sequencing. Materials and Methods: Samples were obtained using a syringe or a periopaper from periodontal abscesses of 20 volunteers who met the research criteria. The three different bacterial colonies that were observed most intensely in each sample were selected and purified, and the isolates obtained were kept until the next characterization. Genomic DNA was isolated from each isolate; 16S rRNA genes were amplified by polymerase chain reaction and identified using DNA sequencing analyses. Results: As a result of culture-dependent methods, bacterial species belonging to Streptococcus, Staphylococcus, Neisseria, Actinomyces, Morococcus, Moraxella, and Enterococcus genera were isolated from a total of 60 bacterial isolates, three of which were the most densely growing colonies from each periodontal abscess sample. Conclusion: In our study, most of the bacterial species detected were identified for the first time in the bacterial content of periodontal abscesses. In some previously done studies, most of these bacteria species were shown to cause abscesses in different parts of the body. It was concluded that further studies are needed to determine the number and proportion of these bacteria species in total bacterial content to evaluate whether they cause periodontal abscesses.

scholarly journals Humans differ in their personal microbial cloud

PeerJ ◽  
2015 ◽  
Vol 3 ◽  
pp. e1258 ◽  
Author(s):  
James F. Meadow ◽  
Adam E. Altrichter ◽  
Ashley C. Bateman ◽  
Jason Stenson ◽  
GZ Brown ◽  
...  
Keyword(s):  
16S Rrna ◽  
Indoor Air ◽  
Direct Contact ◽  
High Throughput Sequencing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Climate Chamber ◽  
Single Person ◽  
First Time

Dispersal of microbes between humans and the built environment can occur through direct contact with surfaces or through airborne release; the latter mechanism remains poorly understood. Humans emit upwards of 106biological particles per hour, and have long been known to transmit pathogens to other individuals and to indoor surfaces. However it has not previously been demonstrated that humans emit a detectible microbial cloud into surrounding indoor air, nor whether such clouds are sufficiently differentiated to allow the identification of individual occupants. We used high-throughput sequencing of 16S rRNA genes to characterize the airborne bacterial contribution of a single person sitting in a sanitized custom experimental climate chamber. We compared that to air sampled in an adjacent, identical, unoccupied chamber, as well as to supply and exhaust air sources. Additionally, we assessed microbial communities in settled particles surrounding each occupant, to investigate the potential long-term fate of airborne microbial emissions. Most occupants could be clearly detected by their airborne bacterial emissions, as well as their contribution to settled particles, within 1.5–4 h. Bacterial clouds from the occupants were statistically distinct, allowing the identification of some individual occupants. Our results confirm that an occupied space is microbially distinct from an unoccupied one, and demonstrate for the first time that individuals release their own personalized microbial cloud.

scholarly journals Non-Saccharomyces as a tool for modulating wine quality and stimulating malolactic fermentation

2021 ◽  
Author(s):  
Aitor Balmaseda ◽  
Alba Martín-García ◽  
Miguel Ángel Leal ◽  
Nicolas Rozès ◽  
Albert Bordons ◽  
...  
Keyword(s):  
Alcoholic Fermentation ◽  
Malolactic Fermentation ◽  
Oenococcus Oeni ◽  
Starter Cultures ◽  
Wine Quality ◽  
Saccharomyces Yeasts

Recent research in non-Saccharomyces yeasts promotes their use as starter cultures in wine alcoholic fermentation together with S. cerevisiae. The use of these non-conventional yeasts can modulate the organoleptic profile of wines. However, it is unclear how they will modulate wines together with Oenococcus oeni after malolactic fermentation. In this article we discuss the main oenological consequences of these interactions and how malolactic fermentation can be stimulated using some of these non-Saccharomyces yeasts.

scholarly journals Effect of antibiotics on the cellulolytic and nitrification activity of gray forest soil

2021 ◽  
Vol 15 (4) ◽  
pp. 52-62
Author(s):  
T. A. Trifonova ◽  
A. G. Kosmacheva ◽  
S. M. Chesnokova
Keyword(s):  
Forest Soil ◽  
Gray Forest Soil ◽  
Inhibitory Effect ◽  
Taxonomic Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Laboratory Model ◽  
Cellulolytic Activity ◽  
Nitrification Activity ◽  
Ribosomal Operons

Aim. To investigate the effect of certain antibiotics - tylosin, oxytetracycline and benzylpenicillin - on the potential nitrifying and cellulolytic activity of gray forest soil using laboratory model research methods.Material and Methods. The object of the research was agricultural gray forest medium loamy soil. The study was carried out by conducting laboratory model experiments. The analysed samples were incubated at 27°C and in the absence of illumination for 30 days and then subsequently analysed for cellulolytic activity (by the application method) and nitrification activity (by the potentiometric method). The taxonomic composition of the bacterial community of the studied soil was established based on analysis of amplicon libraries of fragments of ribosomal operons of 16S rRNA genes by the NGS method.Results. The largest number of nitrification organisms in the soil studied were archaea of the family Nitrososphaeraceae which are autotrophic ammonium oxidants. Most resistant to the effects of the antibiotics used was cellulolytic activity which was suppressed only by the addition of tylosin and its admixture with oxytetracycline. The nitrification activity of the soil varied depending on the concentration and preparations applied, the greatest inhibitory effect being exerted by tylosin. Antibiotic mixtures slightly enhanced the nitrification process at 50-100 mg/kg and were suppressed in the range of 150-700 mg/kg. Conclusion. Once in the soil, the antibiotics studied are capable of both stimulating and inhibiting enzymatic processes. Mixtures of antibiotics rather than their individual applications produce the greatest impact. In medium loamy gray forest soil the presence of antibiotics is more dangerous to nitrification activity. 

Sign in / Sign up

Export Citation Format

Share Document