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 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 Colonisation of leaf litter by aquatic invertebrates in an Atlantic Forest stream

2014 ◽  
Vol 74 (2) ◽  
pp. 267-273 ◽  
Author(s):  
VC. Oliveira ◽  
EA. Gonçalves ◽  
RG. Alves
Keyword(s):  
Leaf Litter ◽  
Atlantic Forest ◽  
Riparian Vegetation ◽  
Aquatic Invertebrates ◽  
Dry Weight ◽  
Taxonomic Composition ◽  
Β Diversity ◽  
Forest Stream ◽  
Α Diversity ◽  
Abundance And Diversity

Riparian vegetation along streams in the Atlantic Forest in Brazil contributes to the formation of a highly heterogeneous leaf litter in streambeds. To investigate the structure and composition of the aquatic invertebrate community during the process of leaf decomposition of two plant species present along the banks of the stream studied, 21 plastic mesh bags containing 2.5g (dry weight) of leaf matter from each species (Alchornea glandulosa (Vell) and Cabralea canjerana End. and Poeppig), for a total of 5.0g, were placed in the streambed. Three bags were removed after 3, 6, 9, 12, 24, 48 and 96 days. The taxonomic density was negatively correlated with the remaining weight. The high density of collector organisms, such as Chironomidae, Oligochaeta and Amphipoda, on the last day of incubation, probably occurred due to the increased amount of fine organic matter in the more advanced decomposition stages. The highest α diversity (Shannon-Wiener) values were observed for the 3rd and 96th days of the experiment, while the β diversity values showed that these days presented the highest variation in the taxonomic composition, thus presenting a different faunistic composition. This study showed that the trophic structure and composition of aquatic invertebrates changes during the decomposition of leaf litter. The faunistic abundance and diversity observed in this study indicate that the entrance of material from plants growing along streams provides favorable conditions for the colonisation and establishment of invertebrates in lower-order streams, and thus points to the need to preserve riparian vegetation.

scholarly journals Impact of Vitamin D Deficit on the Rat Gut Microbiome

Nutrients ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 2564 ◽  
Author(s):  
Iñaki Robles-Vera ◽  
María Callejo ◽  
Ricardo Ramos ◽  
Juan Duarte ◽  
Francisco Perez-Vizcaino
Keyword(s):  
Vitamin D ◽  
Gut Microbiota ◽  
Vitamin D Deficiency ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
Gut Dysbiosis ◽  
Β Diversity ◽  
Α Diversity ◽  
Rat Gut

Inadequate immunologic, metabolic and cardiovascular homeostasis has been related to either an alteration of the gut microbiota or to vitamin D deficiency. We analyzed whether vitamin D deficiency alters rat gut microbiota. Male Wistar rats were fed a standard or a vitamin D-free diet for seven weeks. The microbiome composition was determined in fecal samples by 16S rRNA gene sequencing. The vitamin D-free diet produced mild changes on α- diversity but no effect on β-diversity in the global microbiome. Markers of gut dysbiosis like Firmicutes-to-Bacteroidetes ratio or the short chain fatty acid producing bacterial genera were not significantly affected by vitamin D deficiency. Notably, there was an increase in the relative abundance of the Enterobacteriaceae, with significant rises in its associated genera Escherichia, Candidatus blochmannia and Enterobacter in vitamin D deficient rats. Prevotella and Actinomyces were also increased and Odoribacteraceae and its genus Butyricimonas were decreased in rats with vitamin D-free diet. In conclusion, vitamin D deficit does not induce gut dysbiosis but produces some specific changes in bacterial taxa, which may play a pathophysiological role in the immunologic dysregulation associated with this hypovitaminosis.

scholarly journals Epidermal Microbiomes of Triakis Semifasciata Are Consistent Across Captive and Wild Environments

2021 ◽  
Author(s):  
Asha Goodman ◽  
Bhavya Papudeshi ◽  
Michael P. Doane ◽  
Colton Johnson ◽  
Maria Mora ◽  
...  
Keyword(s):  
Taxonomic Composition ◽  
Shark Species ◽  
Wild Populations ◽  
Microbiome Composition ◽  
Α Diversity ◽  
Novel Association ◽  
Species Specific ◽  
La Jolla ◽  
Triakis Semifasciata ◽  
Leopard Sharks

Abstract Background: Characterizations of sharks-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California), semi-captive (<1 year in captivity; Scripps Institute of Oceanography, California) and wild environments (Moss Landing and La Jolla, California). Results: Here we report captive environments do not drive microbiome composition of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as MAGs revealed a consistent relationship across captive, semi-captive, and wild populations. Conclusions: Our report illustrates the importance of conservation programs for coastal fishes as epidermally-associated microbes of near-shore shark species do not suffer detrimental impacts from long or short-term captivity. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel microbial associations that are consistent across captive gradients.

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 Paytuví-Gallart ◽  
Vicente Boix ◽  
...  
Keyword(s):  
Cohort Study ◽  
Retrospective Cohort Study ◽  
Retrospective Cohort ◽  
Mediterranean Area ◽  
Hospitalised Patients

scholarly journals Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder

2020 ◽  
Author(s):  
Laura Domènech ◽  
Jesse Willis ◽  
Maria Alemany ◽  
Marta Morell ◽  
Eva Real ◽  
...  
Keyword(s):  
Obsessive Compulsive Disorder ◽  
Relative Abundance ◽  
Brain Activity ◽  
Metagenomic Sequencing ◽  
Obsessive Compulsive ◽  
Microbiome Composition ◽  
Compulsive Disorder ◽  
Β Diversity ◽  
Α Diversity ◽  
And Gender

ABSTRACTAlthough the etiology of obsessive-compulsive disorder (OCD) is largely unknown, it is accepted that OCD is a complex disorder. There is a known bi-directional interaction between the gut microbiome and brain activity. Several authors have reported associations between changes in gut microbiota and neuropsychiatric disorders, including depression or autism. Furthermore, a pediatric-onset neuropsychiatric OCD-related syndrome occurs after streptococcal infection, which might indicate that exposure to certain microbes could be involved in OCD susceptibility. However, only one study has investigated the microbiome of OCD patients to date. We performed 16S ribosomal RNA gene-based metagenomic sequencing to analyze the stool and oropharyngeal microbiome composition of 32 OCD cases and 32 age and gender matched controls. We estimated different α- and β-diversity measures and performed LEfSe and Wilcoxon tests to assess differences in bacterial distribution. OCD stool samples showed a trend towards lower bacterial α-diversity, as well as an increase of the relative abundance of Rikenellaceae, particularly of the genus Alistipes, and lower relative abundance of Prevotellaceae, and two genera within the Lachnospiraceae: Agathobacer and Coprococcus. However, we did not observe a different Bacteroidetes to Firmicutes ratio between OCD cases and controls. Analysis of the oropharyngeal microbiome composition showed a lower Fusobacteria to Actinobacteria ratio in OCD cases. In conclusion, we observed an imbalance in the gut and oropharyngeal microbiomes of OCD cases, including, in stool, an increase of bacteria from the Rikenellaceae family, associated with gut inflammation, and a decrease of bacteria from the Coprococcus genus, associated with DOPAC synthesis.

Attributes of Physical Activity and Gut Microbiome in Adults: A Systematic Review

2020 ◽  
Vol 41 (12) ◽  
pp. 801-814
Author(s):  
Roy Tzemah Shahar ◽  
Omry Koren ◽  
Sarah Matarasso ◽  
Tamar Shochat ◽  
Faiga Magzal ◽  
...  
Keyword(s):  
Physical Activity ◽  
Gut Microbiome ◽  
Dietary Intervention ◽  
Physical Activity Intervention ◽  
Cochrane Library ◽  
Microbiome Composition ◽  
Muscle Strengthening ◽  
Β Diversity ◽  
Physical Activity Interventions ◽  
Α Diversity

AbstractGrowing evidence shows the contribution of physical activity interventions to the gut microbiome. However, specific physical activity characteristics that can modify the gut microbiome are unknown. This review’s aim was to explore the contribution of physical activity intervention characteristics on human gut microbiome composition, in terms of diversity, specific bacterial groups, and associated gut microbiome metabolites. A literature search in PubMed; Cochrane Library; CINAHL-EBSCO; SCOPUS; Web of Science; ClinicalTrials.gov; PROSPERO; and ProQuest. Five studies met the inclusion criteria of a physical activity intervention duration of at least five weeks, with any description of the type or dose used. All included studies reported an endurance training; two studies used endurance and an additional muscle-strengthening training regimen. All studies reported using a dietary intervention control. Reported gut microbiome α-diversity changes were non-significant, β-diversity changes were mixed (three studies reported an increase, two reported non-significant changes). All studies reported significant changes in the abundances of specific bacterial/archaea groups and bacteria-related metabolites following interventions. In conclusion, physical activity (regardless of specific characteristics) has significant contribution to gut microbiome composition and associated metabolites. There are no current recommendations for physical activity to promote gut microbiome composition. Future studies should focus on the contribution of current recommended physical activity dose to gut microbiome composition.

Taxonomic composition and diversity of the gut microbiota in relation to habitual diet in Korean adults

2020 ◽  
Author(s):  
Hwayoung Noh ◽  
Hwan-Hee Jang ◽  
Gichang Kim ◽  
Semi Zouiouich ◽  
Su-Yeon Cho ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Smoking Status ◽  
Taxonomic Composition ◽  
Alcoholic Beverages ◽  
Rrna Gene ◽  
Fermented Foods ◽  
Korean Adults ◽  
Β Diversity ◽  
Α Diversity ◽  
Habitual Diet

Abstract Background: Little is known of the relationship between the Korean habitual diet and gut microbiota composition. We investigated associations of habitual dietary intake of foods and nutrients with the taxonomic composition and diversity of gut microbiota in 222 Korean adults aged 18-58 years in a cross-sectional study. Gut microbial taxonomic composition and diversity data were obtained by 16S rRNA gene sequencing of bacterial DNA extracted from fecal samples. Habitual diet for the previous year was collected by a validated food frequency questionnaire. Correlations between intakes of food and nutrients and gut microbial taxonomic composition were examined with adjustment for sex, age, body mass index, dietary supplement, smoking status, and sample batch. Specific dietary patterns associated with α-diversity were identified by reduced rank regression. Enterotypes of gut microbiota were explored by principal coordinate analysis based on β-diversity.Results: The intakes of vegetables, fermented legumes, and potatoes were positively associated with the Firmicutes-to-Bacteroidetes (F/B) ratio, while the intakes of noodle products and non-alcoholic beverages were inversely related to the F/B ratio (all P<0.05). A dietary pattern associated with higher α-diversity (HiαDP) was characterized by greater intakes of fermented legumes, vegetables, potatoes, tea, and fruit/fruit juice and lower intakes of non-alcoholic beverages. Among three different enterotypes identified based on the β-diversity, the Ruminococcus enterotype had higher scores of the HiαDP and was more strongly associated with intakes of vegetables and nuts/seeds, compared to the two other enterotypes. Conclusions: We conclude that the habitual diet in Korean adults was associated with gut microbial taxonomic composition and diversity. A higher intake of plant-based and fermented foods was associated with distinct gut microbial enterotypes in Korean adults.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

scholarly journals Clinical, behavioural and social factors associated with racial disparities in COVID-19 patients from an integrated healthcare system in Georgia: a retrospective cohort study

BMJ Open ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. e044052
Author(s):  
Felipe Lobelo ◽  
Alan Bienvenida ◽  
Serena Leung ◽  
Armand Mbanya ◽  
Elizabeth Leslie ◽  
...  
Keyword(s):  
Quality Of Care ◽  
Racial Disparities ◽  
Clinical Outcomes ◽  
Healthcare System ◽  
Retrospective Cohort ◽  
Chronic Obstructive ◽  
Integrated Healthcare ◽  
Icu Admission ◽  
Hospitalised Patients

ObjectivesTo identify sociodemographic, clinical and behavioural drivers of racial disparities and their association with clinical outcomes among Kaiser Permanente Georgia (KPGA) members with COVID-19.DesignRetrospective cohort of patients with COVID-19 seen from 3 March to 29 October 2020. We described the distribution of underlying comorbidities, quality of care metrics, demographic and social determinants of health (SDOH) indicators across race groups. We also described clinical outcomes in hospitalised patients including length of stay, intensive care unit (ICU) admission, readmission and mortality. We performed multivariable analyses for hospitalisation risk among all patients with COVID-19 and stratifyied by race and sex.SettingKPGA, an integrated healthcare system.Participants5712 patients who all had laboratory-confirmed COVID-19. Of them, 57.8% were female, 58.4% black, 29.5% white, 8.5% Hispanic and 3.6% Asian.ResultsBlack patients had the highest proportions of living in neighborhoods under the federal poverty line (12.4%) and in more deprived locations (neighbourhood deprivation index=0.4). Overall, 14.4% (n=827) of this cohort was hospitalised. Asian patients had the highest rates of ICU admission (53.1%) and mechanical ventilation (21.9%). Among all patients, Hispanics (adjusted 1.60, 95% CI (1.08, 2.37)), blacks (1.43 (1.13, 1.83)), age in years (1.03 (1.02, 1.04)) and living in a zip code with high unemployment (1.08 (1.03, 1.13)) were associated with higher odds of hospitalisation. COVID-19 patients with chronic obstructive pulmonary disease (2.59 (1.67, 4.02)), chronic heart failure (1.79 (1.31, 2.45)), immunocompromised (1.77 (1.16, 2.70)), with glycated haemoglobin >8% (1.68 (1.19, 2.38)), depression (1.60 (1.24, 2.06)), hypertension (1.5 (1.21, 1.87)) and physical inactivity (1.25 (1.03, 1.51)) had higher odds of hospitalisation.ConclusionsBlack and Hispanic KPGA patients were at higher odds of hospitalisation, but not mortality, compared with other race groups. Beyond previously reported sociodemographics and comorbidities, factors such as quality of care, lifestyle behaviours and SDOH indicators should be considered when designing and implementing interventions to reduce COVID-19 racial disparities.

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