scholarly journals Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System

2021 ◽  
Vol 12 ◽  
Author(s):  
Yousri Abdelhafiz ◽  
Jorge M. O. Fernandes ◽  
Simone Larger ◽  
Davide Albanese ◽  
Claudio Donati ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Nile Tilapia ◽  
16S Rrna Gene Sequencing ◽  
Study Groups ◽  
Breeding Strategy ◽  
Rrna Gene ◽  
Beneficial Bacteria ◽  
Core Microbiome ◽  
Recirculating Aquaculture ◽  
Opportunistic Bacteria

In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.

scholarly journals Characterization of External Mucosal Microbiomes of Nile Tilapia and Grey Mullet Co-cultured in Semi-Intensive Pond Systems

2021 ◽  
Vol 12 ◽  
Author(s):  
Ahmed Elsheshtawy ◽  
Benjamin Gregory James Clokie ◽  
Amaya Albalat ◽  
Allan Beveridge ◽  
Ahmad Hamza ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Nile Tilapia ◽  
Pond Water ◽  
Rrna Gene ◽  
Grey Mullet ◽  
Core Microbiome ◽  
Bacterial Phyla ◽  
Organ Specific

The external mucosal surfaces of the fish harbor complex microbial communities, which may play pivotal roles in the physiological, metabolic, and immunological status of the host. Currently, little is known about the composition and role of these communities, whether they are species and/or tissue specific and whether they reflect their surrounding environment. Co-culture of fish, a common practice in semi-intensive aquaculture, where different fish species cohabit in the same contained environment, is an easily accessible and informative model toward understanding such interactions. This study provides the first in-depth characterization of gill and skin microbiomes in co-cultured Nile tilapia (Oreochromis niloticus) and grey mullet (Mugil capito) in semi-intensive pond systems in Egypt using 16S rRNA gene-based amplicon sequencing. Results showed that the microbiome composition of the external surfaces of both species and pond water was dominated by the following bacterial phyla: Proteobacteria, Fusobacteriota, Firmicutes, Planctomycetota, Verrucomicrobiota, Bacteroidota, and Actinobacteriota. However, water microbial communities had the highest abundance and richness and significantly diverged from the external microbiome of both species; thus, the external autochthonous communities are not a passive reflection of their allochthonous communities. The autochthonous bacterial communities of the skin were distinct from those of the gill in both species, indicating that the external microbiome is likely organ specific. However, gill autochthonous communities were clearly species specific, whereas skin communities showed higher commonalities between both species. Core microbiome analysis identified the presence of shared core taxa between both species and pond water in addition to organ-specific taxa within and between the core community of each species. These core taxa included possibly beneficial genera such as Uncultured Pirellulaceae, Exiguobacterium, and Cetobacterium and opportunistic potential pathogens such as Aeromonas, Plesiomonas, and Vibrio. This study provides the first in-depth mapping of bacterial communities in this semi-intensive system that in turn provides a foundation for further studies toward enhancing the health and welfare of these cultured fish and ensuring sustainability.

scholarly journals Identification of a Shared Microbiomic and Metabolomic Profile in Systemic Autoimmune Diseases

2019 ◽  
Vol 8 (9) ◽  
pp. 1291 ◽  
Author(s):  
Bellocchi ◽  
Fernández-Ochoa ◽  
Montanelli ◽  
Vigone ◽  
Santaniello ◽  
...  
Keyword(s):  
Autoimmune Diseases ◽  
Lupus Erythematosus ◽  
High Performance ◽  
16S Rrna Gene Sequencing ◽  
Study Groups ◽  
Mass Spectrometry Analysis ◽  
Rrna Gene ◽  
Operating Characteristics ◽  
Systemic Autoimmune Diseases ◽  
Spectrometry Analysis

Dysbiosis has been described in systemic autoimmune diseases (SADs), including systemic lupus erythematosus (SLE), Sjögren’s syndrome (SjS), and primary anti-phosholipid syndrome (PAPS), however the biological implications of these associations are often elusive. Stool and plasma samples from 114 subjects, including in SLE (n = 27), SjS (n = 23), PAPs (n = 11) and undifferentiated connective tissue (UCTD, n = 26) patients, and geographically-matched healthy controls (HCs, n = 27), were collected for microbiome (16s rRNA gene sequencing) and metabolome (high-performance liquid chromatography coupled to mass spectrometry) analysis to identify shared characteristics across diseases. Out of 130 identified microbial genera, a subset of 29 bacteria was able to differentiate study groups (area under receiver operating characteristics (AUROC) = 0.730 ± 0.025). A fair classification was obtained with a subset of 41 metabolic peaks out of 254 (AUROC = 0.748 ± 0.021). In both models, HCs were well separated from SADs, while UCTD largely overlapped with the other diseases. In all of the SADs pro-tolerogenic bacteria were reduced, while pathobiont genera were increased. Metabolic alterations included two clusters comprised of: (a) members of the acylcarnitine family, positively correlating with a Prevotella-enriched cluster and negatively correlating with a butyrate-producing bacteria-enriched cluster; and (b) phospholipids, negatively correlating with butyrate-producing bacteria. These findings demonstrate a strong interaction between intestinal microbiota and metabolic function in patients with SADs.

scholarly journals Interplay between Fungal Infection and Bacterial Associates in the Wax Moth Galleria mellonella under Different Temperature Conditions

2020 ◽  
Vol 6 (3) ◽  
pp. 170
Author(s):  
Vadim Yu Kryukov ◽  
Elena Kosman ◽  
Oksana Tomilova ◽  
Olga Polenogova ◽  
Ulyana Rotskaya ◽  
...  
Keyword(s):  
Fungal Infection ◽  
Bacterial Communities ◽  
Galleria Mellonella ◽  
Fungal Growth ◽  
16S Rrna Gene Sequencing ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Cultivable Bacteria ◽  
Stress Related Genes ◽  
Rrna Gene Sequencing

Various insect bacterial associates are involved in pathogeneses caused by entomopathogenic fungi. The outcome of infection (fungal growth or decomposition) may depend on environmental factors such as temperature. The aim of this study was to analyze the bacterial communities and immune response of Galleria mellonella larvae injected with Cordyceps militaris and incubated at 15 °C and 25 °C. We examined changes in the bacterial CFUs, bacterial communities (Illumina MiSeq 16S rRNA gene sequencing) and expression of immune, apoptosis, ROS and stress-related genes (qPCR) in larval tissues in response to fungal infection at the mentioned temperatures. Increased survival of larvae after C. militaris injection was observed at 25 °C, although more frequent episodes of spontaneous bacteriosis were observed at this temperature compared to 15 °C. We revealed an increase in the abundance of enterococci and enterobacteria in the midgut and hemolymph in response to infection at 25 °C, which was not observed at 15 °C. Antifungal peptide genes showed the highest expression at 25 °C, while antibacterial peptides and inhibitor of apoptosis genes were strongly expressed at 15 °C. Cultivable bacteria significantly suppressed the growth of C. militaris. We suggest that fungi such as C. militaris may need low temperatures to avoid competition with host bacterial associates.

Effect of bamboo vinegar powder as an antibiotic alternative on the digesta bacteria communities of finishing pigs

2018 ◽  
Vol 64 (10) ◽  
pp. 732-743
Author(s):  
Huan Qu ◽  
Yanjie Huang ◽  
Yinghao Shi ◽  
Ying Liu ◽  
Shenglong Wu ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Growth And Development ◽  
Intestinal Microflora ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Finishing Pigs ◽  
Rrna Gene Sequencing ◽  
Bacteria Communities

This study investigated the use for bamboo vinegar powder as an antibiotic alternative in the diet of growing–finishing pigs by examining their digestive bacterial communities. Forty-five Duroc × Landrace × Yorkshire growing–finishing pigs were randomly allocated to five diet groups: 0%, 0.5%, 1.0%, or 1.5% bamboo vinegar levels and antibiotics. After 37 days, the digesta in duodenum of four pigs from each treatment were analyzed for their bacterial community compositions using 16S rRNA gene sequencing. The addition of 1.5% bamboo vinegar powder had an effect on the intestinal microflora most similar to that of antibiotics, indicating its potential to promote the growth and development of finishing pigs. We also found the 1.5% bamboo vinegar powder group to have an increased abundance of Firmicutes/Bacteroidetes compared with the other bamboo vinegar powder groups, which may enhance the ability of the host to absorb food energy and store more body fat. Additionally, the effects of bamboo vinegar powder on promoting the abundances of Lactobacillus and Thalassospira and on inhibiting Streptococcus and Prevotella growth revealed it may play an important role in animal production. Moreover, functional predictions of microbes via PICRUSt indicated that feed supplemented with 1.5% bamboo vinegar powder could promote many vital metabolic pathways.

scholarly journals Loss of bacterial diversity in the sinuses is associated with lower smell discrimination scores

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Kristi Biswas ◽  
Brett Wagner Mackenzie ◽  
Charlotte Ballauf ◽  
Julia Draf ◽  
Richard G. Douglas ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Olfactory Dysfunction ◽  
Rrna Gene ◽  
Olfactory Loss ◽  
Olfactory Impairment ◽  
Rrna Gene Sequencing ◽  
Normal Sense

Abstract Olfactory impairment affects ~ 20% of the population and has been linked to various serious disorders. Microbes in the nasal cavity play a key role in priming the physiology of the olfactory epithelium and maintaining a normal sense of smell by the host. The aim of this study was to explore the link between olfactory dysfunction and nasal bacterial communities. A total of 162 subjects were recruited for this study from a specialized olfactory dysfunction clinic and placed into one of three groups: anosmia, hyposmia or normosmia. Swabs from the nasal middle meatus were collected from each subject then processed for bacterial 16S rRNA gene sequencing. No overall differences in bacterial diversity or composition were observed between the three cohorts in this study. However, the relative abundances of Corynebacterium spp. and Streptococcus spp. were significantly (p < 0.05) different in subjects with olfactory loss. Furthermore, subjects with deficiencies in discriminating between smells (based on discrimination scores) had a lower bacterial diversity (Simpson’s evenness p < 0.05). While these results are preliminary in nature, potential bacterial biomarkers for olfactory loss were identified. These findings need to be further validated and biologically tested in animal models.

scholarly journals Heliconius Butterflies Host Characteristic and Phylogenetically Structured Adult-Stage Microbiomes

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Tobin J. Hammer ◽  
Jacob C. Dickerson ◽  
W. Owen McMillan ◽  
Noah Fierer
Keyword(s):  
Bacterial Communities ◽  
Evolutionary Biology ◽  
Adult Stage ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Phylogenetic Structure ◽  
Shotgun Metagenomics ◽  
Microbiome Composition ◽  
Form And Function ◽  
Passion Vine

ABSTRACT Lepidoptera (butterflies and moths) are diverse and ecologically important, yet we know little about how they interact with microbes as adults. Due to metamorphosis, the form and function of their adult-stage microbiomes might be very different from those of microbiomes in the larval stage (caterpillars). We studied adult-stage microbiomes of Heliconius and closely related passion-vine butterflies (Heliconiini), which are an important model system in evolutionary biology. To characterize the structure and dynamics of heliconiine microbiomes, we used field collections of wild butterflies, 16S rRNA gene sequencing, quantitative PCR, and shotgun metagenomics. We found that Heliconius butterflies harbor simple and abundant bacterial communities that are moderately consistent among conspecific individuals and over time. Heliconiine microbiomes also exhibited a strong signal of the host phylogeny, with a major distinction between Heliconius and other butterflies. These patterns were largely driven by differing relative abundances of bacterial phylotypes shared among host species and genera, as opposed to the presence or absence of host-specific phylotypes. We suggest that the phylogenetic structure in heliconiine microbiomes arises from conserved host traits that differentially filter microbes from the environment. While the relative importance of different traits remains unclear, our data indicate that pollen feeding (unique to Heliconius) is not a primary driver. Using shotgun metagenomics, we also discovered trypanosomatids and microsporidia to be prevalent in butterfly guts, raising the possibility of antagonistic interactions between eukaryotic parasites and colocalized gut bacteria. Our discovery of characteristic and phylogenetically structured microbiomes provides a foundation for tests of adult-stage microbiome function, a poorly understood aspect of lepidopteran biology. IMPORTANCE Many insects host microbiomes with important ecological functions. However, the prevalence of this phenomenon is unclear because in many insect taxa, microbiomes have been studied in only part of the life cycle, if at all. A prominent example is butterflies and moths, in which the composition and functional role of adult-stage microbiomes are largely unknown. We comprehensively characterized microbiomes in adult passion-vine butterflies. Butterfly-associated bacterial communities are generally abundant in guts, consistent within populations, and composed of taxa widely shared among hosts. More closely related butterflies harbor more similar microbiomes, with the most dramatic shift in microbiome composition occurring in tandem with a suite of ecological and life history traits unique to the genus Heliconius. Butterflies are also frequently infected with previously undescribed eukaryotic parasites, which may interact with bacteria in important ways. These findings advance our understanding of butterfly biology and insect-microbe interactions generally.

scholarly journals Changes of Bacterial Communities in Response to Prolonged Hydrodynamic Disturbances in the Eutrophic Water-Sediment Systems

2019 ◽  
Vol 16 (20) ◽  
pp. 3868
Author(s):  
Haomiao Cheng ◽  
Ling Cheng ◽  
Liang Wang ◽  
Tengyi Zhu ◽  
Wei Cai ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Aquatic Environments ◽  
Rrna Gene ◽  
Evolutionary Trend ◽  
Ecological Evaluation ◽  
Eutrophic Water ◽  
Rrna Gene Sequencing ◽  
Opposite Tendency

The effects of hydrodynamic disturbances on the bacterial communities in eutrophic aquatic environments remain poorly understood, despite their importance to ecological evaluation and remediation. This study investigated the evolution of bacterial communities in the water–sediment systems under the influence of three typical velocity conditions with the timescale of 5 weeks. The results demonstrated that higher bacterial diversity and notable differences were detected in sediment compared to water using the 16S rRNA gene sequencing. The phyla Firmicutes and γ-Proteobacteria survived better in both water and sediment under stronger water disturbances. Their relative abundance peaked at 36.0%, 33.2% in water and 38.0%, 43.6% in sediment, respectively, while the phylum Actinobacteria in water had the opposite tendency. Its relative abundance grew rapidly in static control (SC) and peaked at 44.8%, and it almost disappeared in disturbance conditions. These phenomena were caused by the proliferation of genus Exiguobacterium (belonging to Firmicutes), Citrobacter, Acinetobacter, Pseudomonas (belonging to γ-Proteobacteria), and hgcI_clade (belonging to Actinobacteria). The nonmetric multidimensional scaling (NMDS) and Venn analysis also revealed significantly different evolutionary trend in the three water-sediment systems. It was most likely caused by the changes of geochemical characteristics (dissolved oxygen (DO) and nutrients). This kind of study can provide helpful information for ecological assessment and remediation strategy in eutrophic aquatic environments.

scholarly journals The Gut Microbial Community of Antarctic Fish Detected by 16S rRNA Gene Sequence Analysis

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Wei Song ◽  
Lingzhi Li ◽  
Hongliang Huang ◽  
Keji Jiang ◽  
Fengying Zhang ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Antarctic Fish ◽  
16S Rrna Gene Sequencing ◽  
Physiological Characteristics ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and a range of fitness in fish, but little is known about the gut microbial community in Antarctic fish. In this study, the composition of intestinal microbial community in four species of Antarctic fish was detected based on 16S rRNA gene sequencing. As a result, 1 004 639 sequences were obtained from 13 samples identified into 36 phyla and 804 genera, in which Proteobacteria, Actinobacteria, Firmicutes, Thermi, and Bacteroidetes were the dominant phyla, and Rhodococcus, Thermus, Acinetobacter, Propionibacterium, Streptococcus, and Mycoplasma were the dominant genera. The number of common OTUs (operational taxonomic units) varied from 346 to 768, while unique OTUs varied from 84 to 694 in the four species of Antarctic fish. Moreover, intestinal bacterial communities in individuals of each species were not really similar, and those in the four species were not absolutely different, suggesting that bacterial communities might influence the physiological characteristics of Antarctic fish, and the common bacterial communities might contribute to the fish survival ability in extreme Antarctic environment, while the different ones were related to the living habits. All of these results could offer certain information for the future study of Antarctic fish physiological characteristics.

scholarly journals Dichotomy between regulation of coral bacterial communities and calcification physiology under ocean acidification conditions

2021 ◽  
Author(s):  
A. Shore ◽  
R. D. Day ◽  
J. A. Stewart ◽  
C.A. Burge
Keyword(s):  
Ocean Acidification ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Ph Gradient ◽  
Rrna Gene ◽  
Seawater Ph ◽  
Coral Health ◽  
And Function ◽  
The Impact

Ocean acidification (OA) threatens the growth and function of coral reef ecosystems. A key component to coral health is the microbiome, but little is known about the impact of OA on coral microbiomes. A submarine CO2 vent at Maug Island in the Northern Marianas Islands provides a natural pH gradient to investigate coral responses to long-term OA conditions. Three coral species (Pocillopora eydouxi, Porites lobata, and Porites rus) were sampled from three sites where mean seawater pH is 8.04, 7.98, and 7.94. We characterized coral bacterial communities (using 16S rRNA gene sequencing) and determined pH of the extracellular calcifying fluid (ECF) (using skeletal boron isotopes) across the seawater pH gradient. Bacterial communities of both Porites species stabilized (decreases in community dispersion) with decreased seawater pH, coupled with large increases in the abundance of Endozoicomonas, an endosymbiont. P. lobata experienced a significant decrease in ECF pH near the vent, whereas P. rus experienced a trending decrease in ECF pH near the vent. By contrast, Pocillopora exhibited bacterial community destabilization (increases in community dispersion), with significant decreases in Endozoicomonas abundance, while its ECF pH remained unchanged across the pH gradient. Our study shows that OA has multiple consequences on Endozoicomonas abundance and suggests that Endozoicomonas abundance may be an indicator of coral response to OA. We reveal an interesting dichotomy between two facets of coral physiology (regulation of bacterial communities and regulation of calcification), highlighting the importance of multidisciplinary approaches to understanding coral health and function in a changing ocean. IMPORTANCE Ocean acidification (OA) is a consequence of anthropogenic CO2 emissions that is negatively impacting marine ecosystems such as coral reefs. OA affects many aspects of coral physiology, including growth (i.e. calcification) and disrupting associated bacterial communities. Coral-associated bacteria are important for host health, but it remains unclear how coral-associated bacterial communities will respond to future OA conditions. We document changes in coral-associated bacterial communities and changes to calcification physiology with long-term exposure to decreases in seawater pH that are environmentally relevant under mid-range IPCC emission scenarios (0.1 pH units). We also find species-specific responses that may reflect different responses to long-term OA. In Pocillopora, calcification physiology was highly regulated despite changing seawater conditions. In Porites spp., changes in bacterial communities do not reflect a breakdown of coral-bacterial symbiosis. Insights into calcification and host-microbe interactions are critical to predicting the health and function of different coral taxa to future OA conditions.

scholarly journals Enterobacter hormaechei in the intestines of housefly larvae promotes host growth by inhibiting harmful intestinal bacteria

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Qian Zhang ◽  
Shumin Wang ◽  
Xinyu Zhang ◽  
Kexin Zhang ◽  
Wenjuan Liu ◽  
...  
Keyword(s):  
Intestinal Flora ◽  
Intestinal Bacteria ◽  
Symbiotic Bacterium ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Beneficial Bacteria ◽  
Enterobacter Hormaechei ◽  
Rrna Gene Sequencing ◽  
Providencia Stuartii ◽  
Gut Microbial Community

Abstract Background As a pervasive insect that transmits a variety of pathogens to humans and animals, the housefly has abundant and diverse microbial communities in its intestines. These gut microbes play an important role in the biology of insects and form a symbiotic relationship with the host insect. Alterations in the structure of the gut microbial community would affect larval development. Therefore, it is important to understand the mechanism regulating the influence of specific bacteria on the development of housefly larvae. Methods For this study we selected the intestinal symbiotic bacterium Enterobacter hormaechei, which is beneficial to the growth and development of housefly larvae, and used it as a probiotic supplement in larval feed. 16S rRNA gene sequencing technology was used to explore the effect of E. hormaechei on the intestinal flora of housefly larvae, and plate confrontation experiments were performed to study the interaction between E. hormaechei and intestinal microorganisms. Results The composition of the gut microflora of the larvae changed after the larvae were fed E. hormaechei, with the abundance of Pseudochrobactrum, Enterobacter and Vagococcus increasing and that of Klebsiella and Bacillus decreasing. Analysis of the structure and interaction of larval intestinal flora revealed that E. hormaechei inhibited the growth of harmful bacteria, such as Pseudomonas aeruginosa, Providencia stuartii and Providencia vermicola, and promoted the reproduction of beneficial bacteria. Conclusions Our study has explored the influence of specific beneficial bacteria on the intestinal flora of houseflies. The results of this study reveal the important role played by specific beneficial bacteria on the development of housefly larvae and provide insight for the development of sustained biological agents for housefly control through interference of gut microbiota. Graphical abstract

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