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.

Demography of the central california population of the Leopard Shark (Triakis semifasciata)

1992 ◽  
Vol 43 (1) ◽  
pp. 183 ◽  
Author(s):  
GM Cailliet
Keyword(s):  
Population Growth ◽  
Reproductive Rate ◽  
Shark Species ◽  
Sandbar Shark ◽  
Lemon Shark ◽  
Carcharhinus Plumbeus ◽  
Net Reproductive Rate ◽  
Leopard Shark ◽  
Triakis Semifasciata ◽  
Leopard Sharks

Demographic analyses can be quite useful for effectively managing elasmobranch fisheries. However, they require valid estimates of age-specific mortality and natality rates, in addition to information on the distribution, abundance, habits and reproduction of the population, to produce reliable estimates of population growth. Because such detailed ecological information is usually unavailable, complete demographic analyses have been completed for only four shark species: the spiny dogfish, Squalus acanthias; the soupfin shark, Galeorhinus australis; the lemon shark, Negaprion brevirostris; and most recently the sandbar shark, Carcharhinus plumbeus. In California, reliable estimates of age, growth, mortality, age at maturity, and fecundity are available only for the leopard shark, Triakis semifasciata. A demographic analysis of this species yielded a net reproductive rate (Ro) of 4.467, a generation time (G) of 22.35 years, and an estimate of the instantaneous population growth coefficient (r) of 0.067. If the mean fishing pressure over 10 years (F= 0.084) is included in the survivorship function, Ro and r are reduced considerably, especially if leopard sharks first enter the fishery at early ages. A size limit of 120 cm TL (estimated age 13 years), especially for female sharks, is tentatively proposed for the leopard shark fishery.

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 Fecal Metaproteomics Reveals Reduced Gut Inflammation and Changed Microbial Metabolism Following Lifestyle-Induced Weight Loss

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 726
Author(s):  
Ronald Biemann ◽  
Enrico Buß ◽  
Dirk Benndorf ◽  
Theresa Lehmann ◽  
Kay Schallert ◽  
...  
Keyword(s):  
Metabolic Syndrome ◽  
Weight Loss ◽  
Gut Microbiome ◽  
Taxonomic Composition ◽  
Low Grade ◽  
Gut Inflammation ◽  
Functional Changes ◽  
Microbiome Composition ◽  
Before And After ◽  
Human Proteins

Gut microbiota-mediated inflammation promotes obesity-associated low-grade inflammation, which represents a hallmark of metabolic syndrome. To investigate if lifestyle-induced weight loss (WL) may modulate the gut microbiome composition and its interaction with the host on a functional level, we analyzed the fecal metaproteome of 33 individuals with metabolic syndrome in a longitudinal study before and after lifestyle-induced WL in a well-defined cohort. The 6-month WL intervention resulted in reduced BMI (−13.7%), improved insulin sensitivity (HOMA-IR, −46.1%), and reduced levels of circulating hsCRP (−39.9%), indicating metabolic syndrome reversal. The metaprotein spectra revealed a decrease of human proteins associated with gut inflammation. Taxonomic analysis revealed only minor changes in the bacterial composition with an increase of the families Desulfovibrionaceae, Leptospiraceae, Syntrophomonadaceae, Thermotogaceae and Verrucomicrobiaceae. Yet we detected an increased abundance of microbial metaprotein spectra that suggest an enhanced hydrolysis of complex carbohydrates. Hence, lifestyle-induced WL was associated with reduced gut inflammation and functional changes of human and microbial enzymes for carbohydrate hydrolysis while the taxonomic composition of the gut microbiome remained almost stable. The metaproteomics workflow has proven to be a suitable method for monitoring inflammatory changes in the fecal metaproteome.

scholarly journals Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study)

2021 ◽  
Author(s):  
Marc Oliva ◽  
Pierre H. H. Schneeberger ◽  
Victor Rey ◽  
Matthew Cho ◽  
Rachel Taylor ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Taxonomic Composition ◽  
Oropharyngeal Squamous Cell Carcinoma ◽  
Oral Microbiome ◽  
Metagenomic Sequencing ◽  
Α Diversity ◽  
16S Rna ◽  
The Impact

Abstract Background Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT). Methods Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity. Results A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R2 = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use. Conclusions Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.

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 Microbial control of host gene regulation and the evolution of host–microbiome interactions in primates

2020 ◽  
Vol 375 (1808) ◽  
pp. 20190598 ◽  
Author(s):  
Laura Grieneisen ◽  
Amanda L. Muehlbauer ◽  
Ran Blekhman
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Host Species ◽  
Evolutionary Dynamics ◽  
Microbial Control ◽  
Host Gene ◽  
Primate Species ◽  
Microbiome Composition ◽  
Wide Range ◽  
Species Specific

Recent comparative studies have found evidence consistent with the action of natural selection on gene regulation across primate species. Other recent work has shown that the microbiome can regulate host gene expression in a wide range of relevant tissues, leading to downstream effects on immunity, metabolism and other biological systems in the host. In primates, even closely related host species can have large differences in microbiome composition. One potential consequence of these differences is that host species-specific microbial traits could lead to differences in gene expression that influence primate physiology and adaptation to local environments. Here, we will discuss and integrate recent findings from primate comparative genomics and microbiome research, and explore the notion that the microbiome can influence host evolutionary dynamics by affecting gene regulation across primate host species. This article is part of the theme issue ‘The role of the microbiome in host evolution’.

Species-Specific Characteristics Influence Contaminant Accumulation Trajectories and Signatures Across Ontogeny in Three Pelagic Shark Species

2019 ◽  
Vol 53 (12) ◽  
pp. 6997-7006 ◽  
Author(s):  
Kady Lyons ◽  
Dovi Kacev ◽  
Antonella Preti ◽  
David Gillett ◽  
Heidi Dewar ◽  
...  
Keyword(s):  
Shark Species ◽  
Species Specific ◽  
Contaminant Accumulation

Tissue-specific isotope trophic discrimination factors and turnover rates in a marine elasmobranch: empirical and modeling results

2012 ◽  
Vol 69 (3) ◽  
pp. 551-564 ◽  
Author(s):  
Luis Malpica-Cruz ◽  
Sharon Z. Herzka ◽  
Oscar Sosa-Nishizaki ◽  
Juan Pablo Lazo
Keyword(s):  
Natural Populations ◽  
Nitrogen Isotope ◽  
Cartilage Tissue ◽  
Turnover Rates ◽  
Isotopic Equilibrium ◽  
Isotope Turnover ◽  
Discrimination Factors ◽  
Triakis Semifasciata ◽  
Leopard Sharks ◽  
Trophic Discrimination

There are very few studies reporting isotopic trophic discrimination factors and turnover rates for marine elasmobranchs. A controlled laboratory experiment was conducted to estimate carbon and nitrogen isotope trophic discrimination factors and isotope turnover rates for blood, liver, muscle, cartilage tissue, and fin samples of neonate to young-of-the-year leopard sharks ( Triakis semifasciata ). Trophic discrimination factors varied (0.13‰–1.98‰ for δ13C and 1.08‰–1.76‰ for δ15N). Tissues reached or were close to isotopic equilibrium to the new diet after about a threefold biomass gain and 192 days. Liver and blood exhibited faster isotope turnover than muscle, cartilage tissue, and fin samples, and carbon isotopes turned over faster than those of nitrogen. Metabolic turnover contributed substantially to isotopic turnover, which differs from most reports for young marine teleosts. We modeled the relationship between muscle turnover rates and shark size by coupling laboratory results with growth rate estimates for natural populations. Model predictions for small, medium, and large wild leopard sharks indicate the time to isotopic equilibrium is from one to several years.

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