scholarly journals Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics

2021 ◽  
Author(s):  
Kangqi Wu ◽  
Yongtao Xu ◽  
Weiwei Zhang ◽  
Huirong Mao ◽  
Biao Chen ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Microbial Communities ◽  
Sika Deer ◽  
Microbial Composition ◽  
Fecal Microbiome ◽  
Free Range ◽  
And Function ◽  
Metagenomic Approach

We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.

scholarly journals Effects of treatment with enrofloxacin or tulathromycin on fecal microbiota composition and function of dairy calves

2019 ◽  
Author(s):  
Carla Foditsch ◽  
Richard V.V. Pereira ◽  
Julie D. Siler ◽  
Craig Altier ◽  
Lorin D. Warnick
Keyword(s):  
Antimicrobial Resistance ◽  
Antibiotic Resistance Genes ◽  
Study Groups ◽  
Dairy Calves ◽  
Microbiota Composition ◽  
Erythromycin Resistance ◽  
Microbial Composition ◽  
Fecal Microbiome ◽  
Treatment Groups ◽  
And Function

AbstractThe increasing concerns with antimicrobial resistance highlights the need for studies evaluating the impacts of antimicrobial use in livestock on antimicrobial resistance using new sequencing technologies. Through shotgun sequencing, we investigated the changes in the fecal microbiome composition and function, with a focus on functions related to antimicrobial resistance, of dairy calves. Heifers 2 to 3 weeks old, which were not treated with antibiotics by the farm before enrollment, were randomly allocated to one of three study groups: control (no treatment), enrofloxacin, or tulathromycin. Fecal samples were collected at days 4, 14, 56 and 112 days after enrollment, and DNA extraction and sample preparation and sequencing was conducted. The effect of antibiotic treatment on each taxon and functional level by time (including Day 0 as a covariate) revealed few changes in the microbiota. At the genus level, enrofloxacin group had higher abundance of Blautia, Coprococcus and Desulfovibrio and lower abundance of Bacteroides when compared to other treatment groups. The SEED database was used for functional analyses, which showed that calves in the enrofloxacin group started with a higher abundance of “Resistance to antibiotics and toxic compounds” function on Day 0, however an increase in antibiotic resistance genes after treatment with enrofloxacin was not observed. “Resistance to Fluoroquinolones” and “Erythromycin resistance”, of relevance given the study groups, were not statistically different in abundance between treatment groups. “Resistance to fluoroquinolones” increased during the study period regardless of treatment group. Despite small differences over the first weeks between treatment groups, at Day 112 the microbiota composition and functional profile was similar among all study groups. These findings show that metaphylaxis treatment of dairy calves with either enrofloxacin or tulathromycin have minimal impacts on the microbial composition and functional microbiota of dairy calves over time.

scholarly journals Structure and function of the bacterial and fungal gut flora of Neotropical butterflies

2017 ◽  
Author(s):  
Alison Ravenscraft ◽  
Michelle Berry ◽  
Tobin Hammer ◽  
Kabir Peay ◽  
Carol Boggs
Keyword(s):  
Amino Acids ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Microbial Community Composition ◽  
Structure And Function ◽  
Feeding Guilds ◽  
Gut Flora ◽  
Microbial Composition ◽  
Host Diet ◽  
And Function

AbstractThe relationship between animals and their gut flora is simultaneously one of the most common and most complex symbioses on Earth. Despite its ubiquity, our understanding of this invisible but often critical relationship is still in its infancy. We employed adult Neotropical butterflies as a study system to ask three questions: First, how does gut microbial community composition vary across host individuals, species and dietary guilds? Second, how do gut flora compare to food microbial communities? Finally, are gut flora functionally adapted to the chemical makeup of host foods? To answer these questions we captured nearly 300 Costa Rican butterflies representing over 50 species, six families and two feeding guilds: frugivores and nectivores. We characterized the bacteria and fungi in guts, wild fruits and wild nectars via amplicon sequencing and assessed the catabolic abilities of the gut flora via culture-based assays.Gut communities were distinct from food communities, suggesting that the gut environment acts as a strong filter on potential colonists. Nevertheless, gut flora varied widely among individuals and species. On average, a pair of butterflies shared 21% of their bacterial species and 6% of their fungi. Host species explained 25-30% of total variation in microbial communities while host diet explained 4%. However, diet was still relevant at the individual microbe level—half of the most abundant microbial species differed in abundance between frugivores and nectivores. Diet was also related to the functional profile of gut flora: compared to frugivores, nectivores’ gut flora exhibited increased catabolism of sugars and sugar alcohols and decreased catabolism of amino acids, carboxylic acids and dicarboxylic acids. Since fermented juice contains more amino acids and less sugar than nectar, it appears that host diet filters the gut flora by favoring microbes that digest compounds abundant in foods.By quantifying the degree to which gut communities vary among host individuals, species and dietary guilds and evaluating how gut microbial composition and catabolic potential are related to host diet, this study deepens our understanding of the structure and function of one of the most complex and ubiquitous symbioses in the animal kingdom.

scholarly journals Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

2021 ◽  
Vol 12 ◽  
Author(s):  
Ludek Sehnal ◽  
Elizabeth Brammer-Robbins ◽  
Alexis M. Wormington ◽  
Ludek Blaha ◽  
Joe Bisesi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Aquatic Ecosystems ◽  
Marine Mammals ◽  
Integrative Approach ◽  
Aquatic Animal ◽  
Gastrointestinal Microbiota ◽  
Microbial Composition ◽  
Aquatic Vertebrates ◽  
And Function ◽  
The Impact

Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.

scholarly journals Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms

2019 ◽  
Author(s):  
Philipp Rausch ◽  
Malte Rühlemann ◽  
Britt Hermes ◽  
Shauni Doms ◽  
Tal Dagan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Microbial Composition ◽  
Evolutionary Patterns ◽  
Wide Range ◽  
Taxonomic Groups ◽  
And Function

AbstractBackgroundThe interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution and development of both players. These interdependencies inspired a new view of multicellular organisms as “metaorganisms”. The goal of the Collaborative Research Center “Origin and Function of Metaorganisms” is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.MethodsIn order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon- and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.ConclusionWhile 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods and that metagenomic shotgun results are largely dependent on the employed pipeline. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.

scholarly journals Loss of a Single Plant Functional Group in Litter Had Marginal Impacts on Microbial Community Diversity and Composition in a Tibet Fir Forest

2021 ◽  
Author(s):  
Qianwei Li ◽  
Lifeng Wang ◽  
Yamei Chen ◽  
Li Guo ◽  
Chengming You ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Driving Forces ◽  
Community Diversity ◽  
Plant Functional Groups ◽  
Plant Residues ◽  
Microbial Composition ◽  
Ecological Processes ◽  
And Function

Abstract Aim The decomposition of plant residues is a fundamental process of soil organic matter accumulation. The loss of plant functional groups (PFGs) could affect this process by producing litter of different qualities in the soil. Microorganisms are one of the indispensable driving forces of ecological processes, but the mechanisms by microbial communities respond to aboveground PFG changes are still unclear, which limits our understanding of biogeochemical cycle changes under PFG loss.Methods We assessed the microbial taxonomic and functional composition of six typical single PFGs (evergreen conifer, evergreen shrubs, deciduous shrub, graminoid, forb and fern), random loss of a single PFG (SPFG) from litter mixtures and total mixture of six PFGs in a Tibetan fir forest by a high-throughput sequencing method.Results The microbial composition and function did not change with loss of a SPFG in litter, and microbial communities were mainly determined by the carbon and nitrogen ratio (C:N), carbon and phosphorus ratio (C:P), N and lignin, and bacterial functional pathways and fungal functional guilds were both determined by N, C:N and C:P ratios. Bacterial diversity was positively related while fungal diversity was negatively related to N and cellulose concentrations.Conclusion We speculated that the difference in initial litter qualities (especially C:N) between different PFGs, rather than a decreased number of PFGs, is a determinant of microbial composition and function. As the loss of PFG does not change litter quality, the microbial community can resist the loss of PFG, which maintains alpine ecosystem carbon and nutrient cycling stability.

scholarly journals Evaluation of acidogenesis products’ effect on biogas production performed with metagenomics and isotopic approaches

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Anna Detman ◽  
Michał Bucha ◽  
Laura Treu ◽  
Aleksandra Chojnacka ◽  
Łukasz Pleśniak ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Production ◽  
Bacterial Species ◽  
Stable Carbon Isotope ◽  
Anaerobic Sludge ◽  
Methane Formation ◽  
Microbial Composition ◽  
Fermentation Products ◽  
Core Microbiome ◽  
Specific Species

Abstract Background During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. Results Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%–67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. Conclusions In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

scholarly journals Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shenzheng Zeng ◽  
Sukontorn Khoruamkid ◽  
Warinphorn Kongpakdee ◽  
Dongdong Wei ◽  
Lingfei Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Well Being ◽  
Pacific White Shrimp ◽  
Shrimp Farming ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Water And Sediment ◽  
Surrounding Environment ◽  
Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

scholarly journals Exploring the microbiome in health and disease

2017 ◽  
Vol 1 ◽  
pp. 239784731774188 ◽  
Author(s):  
Elena Scotti ◽  
Stéphanie Boué ◽  
Giuseppe Lo Sasso ◽  
Filippo Zanetti ◽  
Vincenzo Belcastro ◽  
...  
Keyword(s):  
Human Health ◽  
Metabolic Diseases ◽  
Skin Diseases ◽  
Human Microbiome ◽  
Chronic Obstructive ◽  
Microbial Composition ◽  
Obstructive Pulmonary Disease ◽  
New Findings ◽  
Dynamics And Function ◽  
And Function

The analysis of human microbiome is an exciting and rapidly expanding field of research. In the past decade, the biological relevance of the microbiome for human health has become evident. Microbiome comprises a complex collection of microorganisms, with their genes and metabolites, colonizing different body niches. It is now well known that the microbiome interacts with its host, assisting in the bioconversion of nutrients and detoxification, supporting immunity, protecting against pathogenic microbes, and maintaining health. Remarkable new findings showed that our microbiome not only primarily affects the health and function of the gastrointestinal tract but also has a strong influence on general body health through its close interaction with the nervous system and the lung. Therefore, a perfect and sensitive balanced interaction of microbes with the host is required for a healthy body. In fact, growing evidence suggests that the dynamics and function of the indigenous microbiota can be influenced by many factors, including genetics, diet, age, and toxicological agents like cigarette smoke, environmental contaminants, and drugs. The disruption of this balance, that is called dysbiosis, is associated with a plethora of diseases, including metabolic diseases, inflammatory bowel disease, chronic obstructive pulmonary disease, periodontitis, skin diseases, and neurological disorders. The importance of the host microbiome for the human health has also led to the emergence of novel therapeutic approaches focused on the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful roles. In the present review, we outline recent studies devoted to elucidate not only the role of microbiome in health conditions and the possible link with various types of diseases but also the influence of various toxicological factors on the microbial composition and function.

scholarly journals Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Daniela Rosado ◽  
Raquel Xavier ◽  
Jo Cable ◽  
Ricardo Severino ◽  
Pedro Tarroso ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Diversity ◽  
Water Temperature ◽  
Abiotic Factors ◽  
Seasonal Effect ◽  
Microbial Composition ◽  
Surrounding Water ◽  
European Seabass ◽  
And Function ◽  
The Impact

AbstractFish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

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