scholarly journals Effect of homeopathic medicines on growth, survival and gastrointestinal microbiota of juvenile scallop Argopecten ventricosus

2019 ◽  
pp. 7328-7338
Author(s):  
José Manuel Mazón-Suástegui ◽  
Dariel Tovar-Ramírez ◽  
Nadia Livia Ortíz-Cornejo ◽  
Milagro García-Bernal ◽  
Jesús Antonio López-Carvallo ◽  
...  
Keyword(s):  
Species Level ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gastrointestinal Microbiota ◽  
Clear Separation ◽  
Juvenile Scallop ◽  
Potential Applicability ◽  
Overall Performance ◽  
First Time ◽  
Argopecten Ventricosus

Objective. To study the effect of homeopathic medicines on growth, survival and gastrointestinal (GIT) microbiota of Catarina scallop Argopecten ventricosus. Materials and methods. Five homeopathic treatments (T1) ViP-ViA 1D, (T2) ViP-ViA 7C, (T3) AcF-MsS 1D, (T4) PhA-SiT 7C, (T5) ViT 31C and three controls: (C1) diluted ethanol 1:99, (C2) diluted/succussed ethanol 1C and (C3) distilled water were evaluated (21 days) in triplicate. Microbiota was analysed by sequencing the V3-V5 region of the 16S rRNA genes. Results. The best growth in shell-length corresponded to T1 (117 µm d-1) and T2 (108 µm d-1) and the highest survival (P ≤ 0.05) to T3 and T5, stating T3 as the best HOM-treatment. A clear separation was found in rarefaction curves of HOM-treated against un-treated control scallops. Significant differences (P ≤ 0.05) were found for Phyla (Proteobacteria> Actinobacteria> Firmicutes> Bacterloidetes>Chloroflexi and for Genera: Symbiobacterium> Microbacterium> Methylobacillus> Bacillus> Paenibacillus> Burkholderia> Nostoc> Methylobacterium> Leucobacter). The genus Symbiobacterium was dominant in the HOM-treatment T5 (Vidatox®), finding significant differences (P ≤ 0.05) with respect to all treatments. At species level, Microbacterium maritypicum (Actinobacteria) showed a greater relative abundance (P ≤ 0.05) in T1 and T3 and Symbiobacterium toebii (Firmicutes) was also significantly higher (P ≤ 0.05) in abundance in T5 and T2, both against initial T0. Conclusions. This study showed for the first time, the composition of the GIT microbiota in Catarina scallop A. ventricosus and focused on the potential applicability of homeopathic medicines to improve overall performance and modulate the GIT microbiota of the species.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

scholarly journals PHYLOGENETIC RELATIONSHIPS OF LEPTOBRACHIUM HASSELTII TSCHUDI, 1838 (AMPHIBIA, ANURA, MEGOPHRYIDAE) - DETECTION OF A POSSIBLE CRYPTIC SPECIES

TREUBIA ◽  
2018 ◽  
Vol 44 ◽  
pp. 15 ◽  
Author(s):  
Amir Hamidy ◽  
Masafumi Matsui
Keyword(s):  
Sequence Data ◽  
Taxonomic Status ◽  
Species Level ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
12S Rrna ◽  
The West ◽  
Major Clade ◽  
Dna Phylogeny ◽  
Acoustic Data

By examining mitochondrial DNA phylogeny using 2424bp of sequence data 12S rRNA, tRNAval, and 16S rRNA genes, we evaluated the taxonomic relationships among Javan litter frogs Leptobrachium hasseltii from southern Sumatra, Java, and Bali. Leptobrachium hasseltii formed a well-supported monophyletic group, which comprised two major clades. One major clade represented the southern Sumatran and Javan populations and the other consisted of the population from Bali. The Javan and southern Sumatran clade included two subclades: the West Javan-southern Sumatran group and the Central Javan group. The genetic divergence between the two major clades (Bali vs. Java-Sumatra) suggested their separation happen at species level. Further studies using morphological and acoustic data are needed to determine the taxonomic status of Bali population.

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 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 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.

Effect of gastrointestinal microbiome and its diversity on the expression of tumor-infiltrating lymphocytes in breast cancer.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e14187-e14187
Author(s):  
Jiajie Shi ◽  
Cuizhi Geng
Keyword(s):  
Breast Cancer ◽  
Clinical Characteristics ◽  
Tumor Infiltrating Lymphocytes ◽  
Species Level ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gastrointestinal Microbiome ◽  
Β Diversity ◽  
Infiltrating Lymphocytes ◽  
The Relationship

e14187 Background: The diversity of gastrointestinal microbiome is closely related to human health. In the present study, we compared gastrointestinal microbiome and tumor-infiltrating lymphocytes (TILs) in breast cancer (BC) patients. Methods: A total of 80 BC patients were divided into three groups based on the expression of TILs as follows: high expression of TILs (TIL-H), medium expression of TILs (TIL-M) and low expression of TILs (TIL-L). DNA of gastrointestinal microbiome was determined by Illumina sequencing and taxonomy of 16S rRNA genes. Kruskal-Wallis test and UniFrac analysis of β-diversity were applied to assess the relationship between patients’ clinical characteristics and diversity of gastrointestinal microbiome. Results: The β-diversity distribution was statistically significant (weighted UniFrac P < 0.01, unweighted UniFac P < 0.01) when comparing between the TIL-L and TIL-H groups or among the three groups (TIL-H vs. TIL-M vs. TIL-L). At the genus level, higher abundances of Mycobacterium, Rhodococcus, Catenibacterium, Bulleidia, Anaerofilum, Sneathia, Devosia and TG5 but lower abundances of Methanosphaera and Anaerobiospirillum ( P < 0.05) were identified in the TIL-L group compared with the TIL-H group . At the species level, the species of stercoris, barnesiae, coprophilus, flavefaciens and C21_c20 displayed a higher abundance in the TIL-L group, while producta and komagatae exhibited a greater abundance in the TIL-H group ( P < 0.05). Conclusions: Collectively, the diversity of gastrointestinal microbiome was related to the expression of TILs in BC patients.

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 AB0824 ANALYSIS OF GUT MICROBIOTA IN RHEUMATOID ARTHRITIS PATIENTS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1436.1-1436
Author(s):  
Q. Wang ◽  
S. X. Zhang ◽  
J. Qiao ◽  
G. Shi ◽  
R. Zhao ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gut Microbiota ◽  
Intestinal Flora ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Shanxi Province ◽  
Gastrointestinal Microbiota ◽  
Hematopoietic Stem ◽  
Variable Regions ◽  
And Function

Background:Gastrointestinal microbiota, particularly gut microbiota is an indispensable environmental factor in the progression of Rheumatoid Arthritis (RA). Understanding the diversity and function of the intestinal flora in patients with RA is part and parcel to understand the relationship between microbiota and human health.Objectives:This study aimed to identify the diversity and function of the intestinal flora in patients with RA.Methods:A total of 166 participants were recruited in this study, comprising 93 RA patients and 73 age and sex-matched healthy controls (HCs). Microbial genome was extracted from approximately 250mg fresh fecal samples from all participants using QIAamp PowerFecal DNA Kit (Qiagen). The V3-V4 variable regions of bacterial 16S rRNA genes were sequenced with the Illumina Miseq PE300 system. Sequence data were compiled and processed using Qiime2. Sequences were grouped into operational taxonomic units (ASVs)1. Microbial diversity was estimated by the Simpson index. PICRUSt2 was used to predict KEGG functional pathway differences between RA and HC intestinal flora functions based on ASV Tables2. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) analysis was performed using LEfSe software to discovery the different intestinal flora and functions between RA and healthy.Results:The alpha-diversity index of Simpson the microbiome in RA patients was lower than that of HCs (Figure 1a, P <0.05). Compared with HCs, bacterial Bacilli and Lactobacillales were more abundant in patients with RA (Figure 1b, P <0.05). In contrast, Marinifilaceae, Peptococcaceae, Peptococcales and Phascolarcto bacterium were less abundant in the RA group (Figure 1b, P <0.05). As shown in Figure 1c, propanoate metabolism, taurine and hypotaurine metabolism, ascorbate and aldarate metabolism, biosynthesis of siderophore group nonribosomal peptides and glutathione metabolism were the most significantly altered pathways in RA (P <0.05). Epithelial cell signaling in Helicobacter pylori infection, RNA transport, RNA degradation and plant-pathogen interaction were the most significantly altered pathways in HC (P <0.05). The different KEGG metabolic pathways were mainly concentrated in carbohydrate and amino acid metabolism.Conclusion:Gut dysbiosis in RA patients mainly characterized by reduced the diversity and impaired abundance of the intestinal flora, which severely influence the metabolism of gastrointestinal microbiota. The discovery of the associated intestinal microbiota of RA may provide a new idea for RA treatment.References:[1]Han L, Zhao K, Li Y, et al. A gut microbiota score predicting acute graft-versus-host disease following myeloablative allogeneic hematopoietic stem cell transplantation. Am J Transplant 2020;20(4):1014-27. doi: 10.1111/ajt.15654 [published Online First: 2019/10/13][2]Liss MA, White JR, Goros M, et al. Metabolic Biosynthesis Pathways Identified from Fecal Microbiome Associated with Prostate Cancer. Eur Urol 2018;74(5):575-82. doi: 10.1016/j.eururo.2018.06.033 [published Online First: 2018/07/17]Acknowledgements:This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).Disclosure of Interests:None declared

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