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 The effect of carbon subsidies on marine planktonic niche partitioning and recruitment during biofilm assembly

2015 ◽  
Author(s):  
Chuck Pepe-Ranney ◽  
Ed Hall
Keyword(s):  
Heterotrophic Bacteria ◽  
Alpha Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Competitive Balance ◽  
Community Membership ◽  
Resource Space ◽  
Plankton Communities ◽  
Planktonic Communities

The influence of resource availability on planktonic and biofilm microbial community membership is poorly understood. Heterotrophic bacteria derive some to all of their organic carbon (C) from photoautotrophs while simultaneously competing with photoautotrophs for inorganic nutrients such as phosphorus (P) or nitrogen (N). Therefore, C inputs have the potential to shift the competitive balance of aquatic microbial communities by increasing the resource space available to heterotrophs (more C) while decreasing the resource space available to photoautotrophs (less mineral nutrients due to increased competition from heterotrophs). To test how resource dynamics affect membership of planktonic communities and assembly of biofilm communities we amended a series of flow-through mesocosms with C to alter the availability of C among treatments. Each mesocosm was fed with unfiltered seawater and incubated with sterilized microscope slides as surfaces for biofilm formation. The highest C treatment had the highest planktonic heterotroph abundance, lowest planktonic photoautotroph abundance, and highest biofilm biomass. We surveyed bacterial 16S rRNA genes and plastid 23S rRNA genes to characterize biofilm and planktonic community membership and structure. Regardless of resource additions, biofilm communities had higher alpha diversity than planktonic communities in all mesocosms. Heterotrophic plankton communities were distinct from heterotrophic biofilm communities in all but the highest C treatment where heterotrophic plankton and biofilm communities resembled each other after 17 days. Unlike the heterotrophs, photoautotrophic plankton communities were different than photoautotrophic biofilm communities in composition in all treatments including the highest C treatment. Our results suggest that although resource amendments affect community membership and structure, microbial lifestyle (biofilm versus planktonic) has a stronger influence on community composition.

Sputum Microbiota in Coal Workers Diagnosed With Pneumoconiosis as Revealed by 16S Metagenomic Sequencing

2020 ◽  
Author(s):  
Vladimir Druzhinin ◽  
Liudmila Matskova ◽  
Pavel Demenkov ◽  
Elizaveta Baranova ◽  
Valentin Volobaev ◽  
...  
Keyword(s):  
Inflammatory Responses ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Occupational Activity ◽  
Metagenomic Sequencing ◽  
Coal Miners ◽  
Active Coal ◽  
Coal Workers ◽  
Generation Sequencing

Abstract Objectives: The microbiome of sputum from former and active coal miners diagnosed with coal worker’s pneumoconiosis (CWP) as compared to healthy controls Methods: Next Generation Sequencing of bacterial 16S rRNA genes obtained from the sputum of CWP subjects.Results: Differences were detected between the sputum microbiomes from the healthy and CWP subjects. We noted a significant decrease in Bacteroidetes and an increase in the level of Proteobacteria.Conclusions: The microbiomes found in sputum from CWP subjects are enriched in bacterial species previously reported to induce pro-inflammatory responses. The profile of the microbiomes correlated mainly to the occupational activity and not to the age of the coal miners.

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 Alterations in the Fecal Microbiome and Metabolome of Horses with Antimicrobial-Associated Diarrhea Compared to Antibiotic-Treated and Non-Treated Healthy Case Controls

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1807
Author(s):  
Carolyn Arnold ◽  
Rachel Pilla ◽  
Keith Chaffin ◽  
Jonathan Lidbury ◽  
Joerg Steiner ◽  
...  
Keyword(s):  
Acid Ethyl Ester ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Controlled Study ◽  
Xanthurenic Acid ◽  
Fecal Microbiome ◽  
Alpha And Beta Diversity ◽  
Microbiome Composition ◽  
Metabolite Profiles ◽  
Matched Case

Diarrhea is an adverse effect of antimicrobial therapy in horses. This matched, case-controlled study compared the fecal microbiome and metabolome of horses on antibiotics that developed diarrhea (AAD, n = 17) to those that did not develop diarrhea (ABX, n = 15) and to a control population not exposed to antibiotics (CON, n = 31). Fecal samples were collected from horses that were matched for diet and antimicrobial agent (including dose, route, and duration of therapy). Illumina sequencing of 16S rRNA genes was performed, and QIIME 2.0 was used to generate alpha and beta diversity metrics. Untargeted metabolomics using GC-MS platforms was performed and analyzed using Metaboanalyst 5.0. Microbiome composition was significantly different in AAD compared to CON (ANOSIM, R = 0.568, p = 0.001) but not to ABX (ANOSIM, R = 0.121, p = 0.0012). AAD and ABX horses had significantly decreased richness and evenness compared to CON horses (p < 0.05). Horses on antimicrobials (AAD and ABX) had significant changes in 14 phyla compared to CON horses. Only Verrucomicrobia distinguished AAD from ABX and CON horses (q = 0.0005). Metabolite profiles of horses with AAD clustered separately from ABX and CON horses. Seven metabolites were found to be significantly different between groups (p < 0.05): L-tyrosine, kynurenic acid, xanthurenic acid, 5-hydroxyindole-3-acetic acid, docosahexaenoic acid ethyl ester, daidzein, and N-acetyltyramine. Metabolite profiles of horses on antimicrobials, especially those with AAD, are altered compared to CON horses.

scholarly journals Nasopharyngeal Microbiota as an early severity biomarker in COVID-19 hospitalised patients: a retrospective cohort study in a Mediterranean area.

2021 ◽  
Author(s):  
Maria Paz Ventero ◽  
Oscar Moreno-Perez ◽  
Carmen Molina-Pardines ◽  
Andreu Paytuvi-Gallart ◽  
Vicente Boix ◽  
...  
Keyword(s):  
Retrospective Cohort ◽  
Invasive Mechanical Ventilation ◽  
Fatal Outcome ◽  
Mediterranean Area ◽  
Taxonomic Composition ◽  
Microbiome Composition ◽  
Tertiary Centre ◽  
Β Diversity ◽  
Hospitalised Patients ◽  
Α Diversity

Background: There is mounting evidence suggesting that the microbiome composition could be different in COVID-19 patients. However, the relationship between microbiota and COVID-19 severity progression is still being assessed. This study aimed to analyse the diversity and taxonomic composition of the nasopharyngeal microbiota, to determine its association with COVID-19 clinical outcome. Methods and Findings: Samples came from a retrospective cohort of adult patients with COVID-19, hospitalised in a tertiary centre. To study the nasopharyngeal microbiota, we utilized 16S rRNA sequencing. Raw sequences were processed by QIIME2. The associations between the microbiota, invasive mechanical ventilation (IMV), and all-cause mortality were analysed by multiple logistic regression (OR; 95%CI), adjusted for age, gender, and comorbidity. 177 patients were included: median age 68.0 years, 57.6% males, 59.3% had a Charlson comorbidity index ≥3, and 89.2% with pneumonia. The microbiota α diversity indexes were lower in patients with a fatal outcome, and this association persisted after adjustment for the main confounders; whereas the β diversity analysis showed a significant clustering, grouping the patients with a fatal outcome. After multivariate adjustment, the presence of Selenomonas spp., Filifactor spp., Actinobacillus spp., or Chroococcidiopsis spp., was associated with a reduced risk of IMV (adjusted OR 0.06[95%CI 0.01–0.047], p = 0.007). Conclusions: The microbiota diversity and taxonomic composition are related to COVID-19 severity. Higher diversity and the presence of certain genera in the nasopharyngeal microbiota seem to be early biomarkers of a favourable clinical evolution in hospitalised patients with moderate to severe SARS-CoV-2 infections.

scholarly journals The Organelle in the Room: Under-annotated Mitochondrial Reads Bias Coral Microbiome Analysis

2021 ◽  
Author(s):  
Dylan Sonett ◽  
Tanya Brown ◽  
Johan Bengtsson-Palme ◽  
Jacqueline L. Padilla-Gamiño ◽  
Jesse R. Zaneveld
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Microbiome Analysis ◽  
Coral Microbiome ◽  
Β Diversity ◽  
Microbial Eukaryotes ◽  
Microbial Taxonomy ◽  
Coral Health

AbstractThe microbiomes of tropical corals are actively studied using 16S rRNA gene amplicons to understand microbial roles in coral health, metabolism, and disease resistance. However, primers targeting bacterial and archaeal 16S rRNA genes may also amplify organelle rRNA genes from the coral, associated microbial eukaryotes, and encrusting organisms. In this manuscript, we demonstrate that standard workflows for annotating microbial taxonomy severely under-annotate mitochondrial sequences in 1272 coral microbiomes from the Earth Microbiome Project. This issue prevents annotation of >95% of reads in some samples and persists when using either Greengenes or SILVA taxonomies. Worse, mitochondrial under-annotation varies between species and across anatomy, biasing comparisons of α- and β-diversity. By supplementing existing taxonomies with diverse mitochondrial rRNA sequences, we resolve ~97% of unique unclassified sequences as mitochondrial, without increasing misannotation in mock communities. We recommend using these extended taxonomies for coral microbiome analysis and encourage vigilance regarding similar issues in other hosts.

scholarly journals Mediation Analysis as a Means of Identifying Dietary Components That Differentially Affect the Fecal Microbiota of Infants Weaned by Modified Baby-Led and Traditional Approaches

2018 ◽  
Vol 84 (18) ◽  
Author(s):  
Claudia Leong ◽  
Jillian J. Haszard ◽  
Blair Lawley ◽  
Anna Otal ◽  
Rachael W. Taylor ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Dietary Fiber ◽  
Complementary Feeding ◽  
Alpha Diversity ◽  
The United States ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Diet Records ◽  
Dietary Components

ABSTRACT The introduction of “solids” (i.e., complementary foods) to the milk-only diet in early infancy affects the development of the gut microbiota. The aim of this study was to determine whether a “baby-led” approach to complementary feeding that encourages the early introduction of an adult-type diet results in alterations of the gut microbiota composition compared to traditional spoon-feeding. The Baby-Led Introduction to SolidS (BLISS) study randomized 206 infants to BLISS (a modified version of baby-led weaning [BLW], the introduction of solids at 6 months of age, followed by self-feeding of family foods) or control (traditional spoon-feeding of purées) groups. Fecal microbiotas and 3-day weighed-diet records were analyzed for a subset of 74 infants at 7 and 12 months of age. The composition of the microbiota was determined by sequencing of 16S rRNA genes amplified by PCR from bulk DNA extracted from feces. Diet records were used to estimate food and dietary fiber intake. Alpha diversity (number of operational taxonomic units [OTUs]) was significantly lower in BLISS infants at 12 months of age (difference [95% confidence interval {CI}] of 31 OTUs [3.4 to 58.5]; P = 0.028), and while there were no significant differences between control and BLISS infants in relative abundances of Bifidobacteriaceae, Enterobacteriaceae, Veillonellaceae, Bacteroidaceae, Erysipelotrichaceae, Lachnospiraceae, or Ruminococcaceae at 7 or 12 months of age, OTUs representing the genus Roseburia were less prevalent in BLISS microbiotas at 12 months. Mediation models demonstrated that the intake of “fruit and vegetables” and “dietary fiber” explained 29% and 25%, respectively, of the relationship between group (BLISS versus control) and alpha diversity. IMPORTANCE The introduction of solid foods (complementary feeding or weaning) to infants leads to more-complex compositions of microbial communities (microbiota or microbiome) in the gut. In baby-led weaning (BLW), infants are given only finger foods that they can pick up and feed themselves—there is no parental spoon-feeding of puréed baby foods—and infants are encouraged to eat family meals. BLW is a new approach to infant feeding that is increasing in popularity in the United States, New Zealand, the United Kingdom, and Canada. We used mediation modeling, commonly used in health research but not in microbiota studies until now, to identify particular dietary components that affected the development of the infant gut microbiota.

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 Diet Modification and Not Timed Feeding Strategies Result in Intestinal Microbiome Alterations (P21-030-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Marie van der Merwe ◽  
Sunita Sharma ◽  
Jade Caldwell ◽  
Nicholas Smith ◽  
Richard Bloomer ◽  
...  
Keyword(s):  
High Fat Diet ◽  
Beta Diversity ◽  
Diversity Index ◽  
Alpha Diversity ◽  
Taxonomic Composition ◽  
Intestinal Microbiome ◽  
Feeding Strategies ◽  
High Fat ◽  
Microbiome Composition ◽  
Intestinal Length

Abstract Objectives Time-restricted feeding strategies have been shown to normalize obesity parameters, even under high fat feeding conditions. The objective of this study is to examine whether timed feeding alters parameters of gut health or intestinal microbiome composition. Methods C57BL/6 male mice were randomized to Chow or a high fat diet (HFD) for 6 weeks, followed by a switch from HFD to 1) Chow (sChow), 2) Purified Vegan – Daniel Fast (DF), 3) HFD ad lib, 4) HFD time restricted (TRF), 5) HFD alternative day fasting (ADF), or 6) HFD 60% caloric restriction (CR) for an additional 8 weeks. Results We observed that body mass gain was reduced for all intervention groups (P ≤ 0.0001). Small intestinal length and cecal weight were increased in Chow, sChow and DF (P ≤ 0.02), while total cecal short chain fatty acid (SCFA) concentration was non-significantly increased for all groups consuming the HFD. Proprionate was specifically increased in the Chow, sChow and DF groups (P ≤ 0.02). Chow fed microbiota remained stable in taxonomic composition and alpha diversity (Shannon diversity index) throughout the study. HF fed microbiota displayed lower alpha diversity along with reduced phylum levels of Bacteroidetes and increase Firmicutes. Animals switched from HF to Chow demonstrated a rapid transition in taxonomic composition, alpha, and beta diversity that initially resembled HF, but clustered closely with Chow by weeks 4 and 8 of intervention. After 8 weeks on the respective dietary protocols, alpha diversity of the DF was most similar to Chow fed animals and also resulted in the largest increase in Bacteriodetes and largest decrease in Firmicutes. Beta diversity (weighted UniFrac) showed Chow, sChow, and DF clustered together, while high fat fed groups (HF, CR, ADF, and TRF) clustered. Compared with HF controls, CR and TRF led to a relative increase in the classes Clostridia, Deferribacteres and Deltaproteobacteria. The taxonomic composition and alpha diversity of ADF fasting resembled HF under fed conditions, while ADF under fasting conditions more closely resembled CR and TRF. Conclusions In conclusion, timed feeding on a high fat diet did not result in significant changes in the microbiome, demonstrating that diet, and not fasting is the major determinant for microbiome composition. Funding Sources University of Memphis & Children's Foundation Research Institute, Memphis.

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