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 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 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 Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 63
Author(s):  
Birgit Wassermann ◽  
Lise Korsten ◽  
Gabriele Berg
Keyword(s):  
Plant Pathogens ◽  
Classical Music ◽  
Antagonistic Effect ◽  
Plant Health ◽  
Control Group ◽  
Rrna Gene ◽  
Native Plant ◽  
Core Microbiome ◽  
The Core ◽  
Sound Vibration

Understanding the plant microbiome is a key for plant health and controlling pathogens. Recent studies have shown that plants are responsive towards natural and synthetic sound vibration (SV) by perception and signal transduction, which resulted in resistance towards plant pathogens. However, whether or not native plant microbiomes respond to SV and the underlying mechanism thereof remains unknown. Within the present study we compared grapevine-associated microbiota that was perpetually exposed to classical music with a non-exposed control group from the same vineyard in Stellenbosch, South Africa. By analyzing the 16S rRNA gene and ITS fragment amplicon libraries we found differences between the core microbiome of SV-exposed leaves and the control group. For several of these different genera, e.g., Bacillus, Kocuria and Sphingomonas, a host-beneficial or pathogen-antagonistic effect has been well studied. Moreover, abundances of taxa identified as potential producers of volatile organic compounds that contribute to sensory characteristics of wines, e.g., Methylobacterium, Sphingomonas, Bacillus and Sporobolomyces roseus, were either increased or even unique within the core music-exposed phyllosphere population. Results show an as yet unexplored avenue for improved plant health and the terroir of wine, which are important for environmentally friendly horticulture and consumer appreciation. Although our findings explain one detail of the long-term positive experience to improve grapevine’s resilience by this unusual but innovative technique, more mechanistic studies are necessary to understand the whole interplay.

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 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 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 Ultrafine particles altered gut microbial population and metabolic profiles in a sex-specific manner in an obese mouse model

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kundi Yang ◽  
Mengyang Xu ◽  
Jingyi Cao ◽  
Qi Zhu ◽  
Monica Rahman ◽  
...  
Keyword(s):  
Ultrafine Particles ◽  
Microbial Population ◽  
Phosphate Buffer Solution ◽  
Biodiesel Fuel ◽  
Control Group ◽  
Obese Mouse ◽  
Rrna Gene ◽  
Obese Mice ◽  
Microbial Composition ◽  
Increased Risk

AbstractEmerging evidence has highlighted the connection between exposure to air pollution and the increased risk of obesity, metabolic syndrome, and comorbidities. Given the recent interest in studying the effects of ultrafine particle (UFP) on the health of obese individuals, this study examined the effects of gastrointestinal UFP exposure on gut microbial composition and metabolic function using an in vivo murine model of obesity in both sexes. UFPs generated from light-duty diesel engine combustion of petrodiesel (B0) and a petrodiesel/biodiesel fuel blend (80:20 v/v, B20) were administered orally. Multi-omics approaches, including liquid chromatography–mass spectrometry (LC–MS) based targeted metabolomics and 16S rRNA gene sequence analysis, semi-quantitatively compared the effects of 10-day UFP exposures on obese C57B6 mouse gut microbial population, changes in diversity and community function compared to a phosphate buffer solution (PBS) control group. Our results show that sex-specific differences in the gut microbial population in response to UFP exposure can be observed, as UFPs appear to have a differential impact on several bacterial families in males and females. Meanwhile, the alteration of seventy-five metabolites from the gut microbial metabolome varied significantly (ANOVA p < 0.05) across the PBS control, B0, and B20 groups. Multivariate analyses revealed that the fuel-type specific disruption to the microbial metabolome was observed in both sexes, with stronger disruptive effects found in females in comparison to male obese mice. Metabolic signatures of bacterial cellular oxidative stress, such as the decreased concentration of nucleotides and lipids and increased concentrations of carbohydrate, energy, and vitamin metabolites were detected. Furthermore, blood metabolites from the obese mice were differentially affected by the fuel types used to generate the UFPs (B0 vs. B20).

scholarly journals The bacterial community of the lone star tick (Amblyomma americanum)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
L. Paulina Maldonado-Ruiz ◽  
Saraswoti Neupane ◽  
Yoonseong Park ◽  
Ludek Zurek
Keyword(s):  
Bacterial Community ◽  
Amblyomma Americanum ◽  
Rrna Gene ◽  
Culturable Bacteria ◽  
Core Microbiome ◽  
Lone Star Tick ◽  
Animal Pathogens ◽  
Wide Range ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low. Methods We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks. Results We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin. Conclusions No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.

The bacteriome of the oral cavity in healthy dogs and dogs with periodontal disease

2022 ◽  
pp. 1-9
Author(s):  
Brook A. Niemiec ◽  
Jerzy Gawor ◽  
Shuiquan Tang ◽  
Aishani Prem ◽  
Janina A. Krumbeck
Keyword(s):  
Oral Cavity ◽  
Periodontal Disease ◽  
Bacterial Species ◽  
Abundant Species ◽  
Rrna Gene ◽  
Core Microbiome ◽  
The Core ◽  
Severe Periodontal Disease ◽  
Healthy Dogs ◽  
V3 Region

Abstract OBJECTIVE To compare the bacteriome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease. ANIMALS Dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease. PROCEDURES The maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the V1–V3 region of the 16S rRNA gene. RESULTS 714 bacterial species from 177 families were identified. The 3 most frequently found bacterial species were Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 samples), and a Campylobacter sp (48/51 samples). The most abundant species were P cangingivalis, Porphyromonas gulae, and an undefined Porphyromonas sp. Porphyromonas cangingivalis and Campylobacter sp were part of the core microbiome shared among the 4 groups, and P gulae, which was significantly enriched in dogs with severe periodontal disease, was part of the core microbiome shared between all groups except dogs without periodontal disease. Christensenellaceae sp, Bacteroidales sp, Family XIII sp, Methanobrevibacter oralis, Peptostreptococcus canis, and Tannerella sp formed a unique core microbiome in dogs with severe periodontal disease. CONCLUSIONS AND CLINICAL RELEVANCE Results highlighted that in dogs, potential pathogens can be common members of the oral cavity bacteriome in the absence of disease, and changes in the relative abundance of certain members of the bacteriome can be associated with severity of periodontal disease. Future studies may aim to determine whether these changes are the cause or result of periodontal disease or the host immune response.

scholarly journals Short- and long-term effects of amoxicillin/clavulanic acid or doxycycline on the gastrointestinal microbiome of growing cats

2021 ◽  
Author(s):  
Evangelia Stavroulaki ◽  
Jan S. Suchodolski ◽  
Rachel Pilla ◽  
Geoffrey T. Fosgate ◽  
Chi-Hsuan Sung ◽  
...  
Keyword(s):  
Clavulanic Acid ◽  
Antibiotic Treatment ◽  
Control Group ◽  
Rrna Gene ◽  
Upper Respiratory Tract ◽  
Long Term Effects ◽  
Microbial Composition ◽  
Increased Risk ◽  
Group 15 ◽  
Amoxicillin Clavulanic Acid

Antibiotic treatment in early life influences gastrointestinal (GI) microbial composition and function. In humans, the resultant intestinal dysbiosis is associated with an increased risk for certain diseases later in life. The objective of this study was to determine the temporal effects of antibiotic treatment on the GI microbiome of young cats. Fecal samples were collected from cats randomly allocated to receive either amoxicillin/clavulanic acid (20 mg/kg q12h) for 20 days (AMC group; 15 cats) or doxycycline (10 mg/kg q24h) for 28 days (DOX group;15 cats) as part of the standard treatment of upper respiratory tract infection. In addition, feces were collected from healthy control cats (CON group;15 cats). All cats were approximately two months of age at enrolment. Samples were collected on days 0 (baseline), 20 or 28 (AMC and DOX, respectively; last day of treatment), 60, 120, and 300. DNA was extracted and sequencing of the 16S rRNA gene and qPCR assays were performed. Fecal microbial composition was different on the last day of treatment for AMC cats, and 1 month after the end of antibiotic treatment for DOX cats, compared to CON cats. Species richness was significantly greater in DOX cats compared to CON cats on the last day of treatment. Abundance of Enterobacteriales was increased, and that of Erysipelotrichi was decreased in cats of the AMC group on the last day of treatment compared to CON cats. The abundance of the phylum Proteobacteria was increased in cats of the DOX group on days 60 and 120 compared to cats of the CON group. Only minor differences in abundances between the treatment groups and the control group were present on day 300. Both antibiotics appear to delay the developmental progression of the microbiome, and this effect is more profound during treatment with amoxicillin/clavulanic acid and one month after treatment with doxycycline. Future studies are required to determine if these changes influence microbiome function and whether they have possible effects on disease susceptibility in cats.

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