scholarly journals Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2412 ◽  
Author(s):  
Darren J. Parris ◽  
Rohan M. Brooker ◽  
Michael A. Morgan ◽  
Danielle L. Dixson ◽  
Frank J. Stewart
Keyword(s):  
Life Stage ◽  
Benthic Habitat ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Surrounding Water ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
Pelagic Larvae ◽  
Before And After ◽  
Host Life

The Pomacentridae (damselfish) and Apogonidae (cardinalfish) are among the most common fish families on coral reefs and in the aquarium trade. Members of both families undergo a pelagic larvae phase prior to settlement on the reef, where adults play key roles in benthic habitat structuring and trophic interactions. Fish-associated microbial communities (microbiomes) significantly influence fish health and ecology, yet little is known of how microbiomes change with life stage. We quantified the taxonomic (16S rRNA gene) composition of whole gut microbiomes from ten species of damselfish and two species of cardinalfish from Lizard Island, Australia, focusing specifically on comparisons between pelagic larvae prior to settlement on the reef versus post-settlement juvenile and adult individuals. On average, microbiome phylogenetic diversity increased from pre- to post-settlement, and was unrelated to the microbial composition in the surrounding water column. However, this trend varied among species, suggesting stochasticity in fish microbiome assembly. Pre-settlement fish were enriched with bacteria of the Endozoicomonaceae, Shewanellaceae, and Fusobacteriaceae, whereas settled fish harbored higher abundances of Vibrionaceae and Pasteurellaceae. Several individual operational taxonomic units, including ones related toVibrio harveyi,Shewanella sp., and unculturedEndozoicomonasbacteria, were shared between both pre and post-settlement stages and may be of central importance in the intestinal niche across development. Richness of the core microbiome shared among pre-settlement fish was comparable to that of settled individuals, suggesting that changes in diversity with adulthood are due to the acquisition or loss of host-specific microbes. These results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families.

scholarly journals Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions

Animals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 4
Author(s):  
Giulietta Minozzi ◽  
Filippo Biscarini ◽  
Emanuela Dalla Costa ◽  
Matteo Chincarini ◽  
Nicola Ferri ◽  
...  
Keyword(s):  
Animal Health ◽  
Control Group ◽  
P Value ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Core Microbiome ◽  
Fecal Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Wide Range

The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition.

scholarly journals Tailings microbial community profile and prediction of its functionality in basins of tungsten mine

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ana Paula Chung ◽  
Carina Coimbra ◽  
Pedro Farias ◽  
Romeu Francisco ◽  
Rita Branco ◽  
...  
Keyword(s):  
Rrna Gene ◽  
Microbial Composition ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
Secondary Sources ◽  
Metabolic Functions ◽  
Processing Pathways ◽  
Tungsten Mine ◽  
Microbial Community Profile ◽  
And Function

AbstractIn a circular economy concept, where more than 300 million tons of mining and quarrying wastes are produced annually, those are valuable resources, supplying metals that are extracted today by other processes, if innovative methods and processes for efficient extraction of these elements are applied. This work aims to assess microbiological and chemical spatial distribution within two tailing basins from a tungsten mine, using a MiSeq approach targeting the 16S rRNA gene, to relate microbial composition and function with chemical variability, thus, providing information to enhance the efficiency of the exploitation of these secondary sources. The tailings sediments core microbiome comprised members of family Anaerolineacea and genera Acinetobacter, Bacillus, Cellulomonas, Pseudomonas, Streptococcus and Rothia, despite marked differences in tailings physicochemical properties. The higher contents of Al and K shaped the community of Basin 1, while As-S-Fe contents were correlated with the microbiome composition of Basin 2. The predicted metabolic functions of the microbiome were rich in genes related to metabolism pathways and environmental information processing pathways. An in-depth understanding of the tailings microbiome and its metabolic capabilities can provide a direction for the management of tailings disposal sites and maximize their potential as secondary resources.

scholarly journals Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Marine Drugs ◽  
2020 ◽  
Vol 18 (6) ◽  
pp. 298
Author(s):  
Alison E. Murray ◽  
Nicole E. Avalon ◽  
Lucas Bishop ◽  
Karen W. Davenport ◽  
Erwan Delage ◽  
...  
Keyword(s):  
Marine Invertebrate ◽  
Bioactive Compound ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Specific Sequence ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Synoicum Adareanum ◽  
Palmerolide A

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

scholarly journals Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

2021 ◽  
Author(s):  
Artur Trzebny ◽  
Anna Slodkowicz-Kowalska ◽  
Johanna Björkroth ◽  
Miroslawa Dabert
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Microsporidian Infection ◽  
Functional Content

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

scholarly journals Host phylogeny and life history stage shape the gut microbiome in dwarf (Kogia sima) and pygmy (Kogia breviceps) sperm whales

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Elizabeth R. Denison ◽  
Ryan G. Rhodes ◽  
William A. McLellan ◽  
D. Ann Pabst ◽  
Patrick M. Erwin
Keyword(s):  
Gut Microbiome ◽  
Life Stage ◽  
Life History Stage ◽  
Rrna Gene ◽  
Sperm Whales ◽  
Microbiome Composition ◽  
Host Health ◽  
Species Specific ◽  
Kogia Sima ◽  
Host Development

Abstract Gut microbiomes perform crucial roles in host health and development, but few studies have explored cetacean microbiomes especially deep divers. We characterized the gut microbiomes of stranded dwarf (Kogia sima) and pygmy (K. breviceps) sperm whales to examine the effects of phylogeny and life stage on microbiome composition and diversity. 16S rRNA gene sequence analysis revealed diverse gut communities (averaging 674 OTUs) dominated by a few symbiont taxa (25 OTUs accounted for 64% of total relative abundance). Both phylogeny and life stage shaped community composition and diversity, with species-specific microbiome differences present early in life. Further analysis showed evidence of microbiome convergence with host maturity, albeit through different processes: symbiont ‘accumulation’ in K. sima and ‘winnowing’ in K. breviceps, indicating different methods of community assembly during host development. Furthermore, culture-based analyses yielded 116 pure cultures matching 25 OTUs, including one isolate positive for chitin utilization. Our findings indicate that kogiid gut microbiomes are highly diverse and species-specific, undergo significant shifts with host development, and can be cultivated on specialized media under anaerobic conditions. These results enhance our understanding of the kogiid gut microbiome and may provide useful information for symbiont assessment in host health.

scholarly journals Gut Microbiome Biomarkers in Adolescent Obesity: a Regional Study

2019 ◽  
Author(s):  
Xuefeng Gao ◽  
Binbin Wu ◽  
Yonglong Pan ◽  
Shaoming Zhou ◽  
Ming Zhang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Gut Microbiome ◽  
Blood Pressure Measurement ◽  
Rrna Gene ◽  
Case Control Studies ◽  
Regional Study ◽  
Microbial Composition ◽  
Bacterial Gene ◽  
Fecal Microbiome ◽  
Microbiome Composition

ABSTRACTPurposeThis study aimed to characterize the gut microbiota in obese Shenzhen adolescents, and evaluate the influence of gender on BMI-related differences in the gut microbiome.MethodsPhysical examinations, blood pressure measurement, serological assay, and body composition evaluation were conducted on two-hundred and five adolescents from Shenzhen. Fecal microbiome composition was profiled via 16S rRNA gene sequencing. A Random Forest (RF) classifier model was built to distinguish the BMI categories based on the gut bacterial composition.ResultsFifty-six taxa consisting mainly of Firmicutes were identified that having significant associations with BMI; two OTUs belonging to Ruminococcaceae and one belonging to Lachnospiraceae had relatively strong positive correlations with body fate rate, waistline, and most of serum biochemical parameters. Based on the 56 BMI-associated OTUs, the RF model showed a robust classification accuracy (AUC 0.96) for predicting the obese phenotype. Gender-specific differences in the gut microbiome composition was obtained, and a lower relative abundance of Odoribacter was particularly found in obese boys. Functional analysis revealed a deficiency in bacterial gene contents related to PPAR signaling pathway in obese subjects for both genders; significantly lower levels of adipocytokine signaling pathway and ethylbenzene degradation were particularly detected in obese girls.ConclusionsThis study revealed unique features of gut microbiome in terms of microbial composition and metabolic functions in obese Shenzhen adolescents. The effect of geographical location, age and gender on the gut microbiome should be carefully considered in case–control studies.

scholarly journals 817. Exploring Microbial Community Alterations during Hospital Animal-Assisted Intervention Programs

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S450-S451
Author(s):  
Kathryn R Dalton ◽  
Karen C Carroll ◽  
Karen C Carroll ◽  
Elizabeth A Grice ◽  
Meghan F Davis
Keyword(s):  
Microbial Community ◽  
Group Therapy ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Therapy Dogs ◽  
Microbial Composition ◽  
Healthcare Facilities ◽  
Therapy Dog ◽  
Therapy Animals ◽  
Before And After

Abstract Background Animal-assisted interventions, or pet therapy, is increasingly used by healthcare facilities given the numerous benefits in various settings. However, therapy animals may serve as vectors of hospital-associated pathogens. Yet, both pathogenic and protective commensal microbes could be transferred between patients and therapy animals. This pilot study aims to quantify the microbial sharing between patients and therapy dogs, and determine if contact level and a decolonization intervention modifies this sharing. Methods We collected pediatric patient and therapy dog nasal samples before and after each group therapy visit. Contact level was based on interaction time and key behaviors. Therapy dog handlers performed normal practices for two control visits, then switched to a decolonization protocol (chlorhexidine shampoo prior to the visit, and chlorhexidine wipes during the visit) for two intervention visits. Sample DNA was sequenced for the 16S rRNA gene V1-3 region to assess microbiota composition and diversity. Results We collected 105 samples (79 from patients and 26 from dogs) over 13 study visits. There was an increase in within-sample (alpha) diversity levels after the visits in patients and dogs in control visits, and an overall decrease in intervention visits. Patients were more similar in their microbial composition (beta diversity) to other patients and to dogs after visits. Patients with higher dog contact were more similar to other patients in control and intervention visits using the unweighted metric, but only in control visits for the weighted metric. Conclusion These findings indicate that microbes are shared between patients and therapy dogs during animal-assisted interventions, shown by the increase in alpha diversity levels and microbial community shifts. High contact increased interactions in all pathways, resulting in greater microbial sharing. With the dog pathway blocked, the intervention reduced spread of unique dog taxa, but sharing still occurred in high contact patients. This shows that, while there is potential for the dog to be a vector, other potential pathways are important for microbial sharing during group therapy visits. Infection control efforts should reflect all possible pathways of microbial transmission. Disclosures All Authors: No reported disclosures

scholarly journals Integrating Dietary Data into Microbiome Studies: A Step Forward for Nutri-Metaomics

Nutrients ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 2978
Author(s):  
Francisca Yáñez ◽  
Zaida Soler ◽  
Manon Oliero ◽  
Zixuan Xie ◽  
Iñigo Oyarzun ◽  
...  
Keyword(s):  
Assessment Tool ◽  
Dietary Assessment ◽  
Intraclass Correlation ◽  
Saturated Fat ◽  
Reference Method ◽  
Wilcoxon Test ◽  
Rrna Gene ◽  
Food Groups ◽  
Microbial Composition ◽  
Microbiome Composition

Diet is recognised as the main driver of changes in gut microbiota. However, linking habitual dietary intake to microbiome composition and activity remains a challenge, leaving most microbiome studies with little or no dietary information. To fill this knowledge gap, we conducted two consecutive studies (n = 84: a first pilot study (n = 40) to build a web-based, semi-quantitative simplified FFQ (sFFQ) based on three 24-h dietary recalls (24HRs); a second study (n = 44) served to validate the newly developed sFFQ using three 24HRs as reference method and to relate gut microbiome profiling (16S rRNA gene) with the extracted dietary and lifestyle data. Relative validation analysis provided acceptable classification and agreement for 13 out of 24 (54%) food groups and 20 out of 29 nutrients (69%) based on intraclass correlation coefficient, cross-classification, Spearman’s correlation, Wilcoxon test, and Bland–Altman. Microbiome analysis showed that higher diversity was positively associated with age, vaginal birth, and intake of fruit. In contrast, microbial diversity was negatively associated with BMI, processed meats, ready-to-eat meals, sodium, and saturated fat. Our analysis also revealed a correlation between food groups or nutrients and microbial composition. Overall, we provide the first dietary assessment tool to be validated and correlated with microbiome data for population studies.

scholarly journals Uncovering the core microbiome and distributions of palmerolide in Synoicum adareanum across the Anvers Island archipelago, Antarctica

2020 ◽  
Author(s):  
Alison Murray ◽  
Nicole Avalon ◽  
Lucas Bishop ◽  
Karen W. Davenport ◽  
Erwan Delage ◽  
...  
Keyword(s):  
Specific Activity ◽  
Marine Invertebrate ◽  
Bioactive Compound ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Specific Sequence ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Synoicum Adareanum

AbstractPolar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganismal diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which the bioactive macrolide that has specific activity to melanoma, palmerolide A (PalA), was found. PalA bears structural resemblance to a combined nonribosomal peptide polyketide, that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64° 46'S, 64° 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island archipelago. The microbiome composition (V3-V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacteria, 20 of which were distinct from regional bacterioplankton. Co-occurrence analysis yielded several potentially interacting subsystems and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. Taking these results together with an analysis of biosynthetic potential of related microbiome taxa indicates a core microbiome with substantial promise for natural product biosynthesis that likely interact with the host and with each other.

scholarly journals The Associations between Diet and Socioeconomic Disparities and the Intestinal Microbiome in Preadolescence

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2645
Author(s):  
Yelena Lapidot ◽  
Leah Reshef ◽  
Rebecca Goldsmith ◽  
Wasef Na’amnih ◽  
Eias Kassem ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Polyunsaturated Fatty Acids ◽  
Dietary Intake ◽  
Growth Period ◽  
Amplicon Sequencing ◽  
Taxonomic Composition ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Microbiome Composition

The intestinal microbiome continues to shift and develop throughout youth and could play a pivotal role in health and wellbeing throughout adulthood. Environmental and interpersonal determinants are strong mediators of the intestinal microbiome during the rapid growth period of preadolescence. We aim to delineate associations between the gut microbiome composition, body mass index (BMI), dietary intake and socioeconomic status (SES) in a cohort of ethnically homogenous preadolescents. This cohort included 139 Arab children aged 10–12 years, from varying socioeconomic strata. Dietary intake was assessed using the 24-h recall method. The intestinal microbiome was analyzed using 16S rRNA gene amplicon sequencing. Microbial composition was associated with SES, showing an overrepresentation of Prevotella and Eubacterium in children with lower SES. Higher BMI was associated with lower microbial diversity and altered taxonomic composition, including higher levels of Collinsella, especially among participants from lower SES. Intake of polyunsaturated fatty acids was the strongest predictor of bacterial alterations, including an independent association with Lachnobacterium and Lactobacillus. This study demonstrates that the intestinal microbiome in preadolescents is associated with socioeconomic determinants, BMI and dietary intake, specifically with higher consumption of polyunsaturated fatty acids. Thus, tailored interventions during these crucial years have the potential to improve health disparities throughout the lifespan.

Sign in / Sign up

Export Citation Format

Share Document