Perturbation and restoration of the fathead minnow gut microbiome after low-level triclosan exposure

Rainbow darter (Etheostoma caeruleum) from a river impacted by municipal wastewater effluents have altered gut content microbiomes

Municipal wastewater treatment plant (WWTP) effluent contains pharmaceuticals and personal care products known to affect fish health and reproduction. The microbiome is a community of bacteria integral in maintaining host health and is influenced by species, diet, and environment. This study investigated changes in the diversity and composition of the gut content microbiome of rainbow darter (Etheostoma caeruleum) at ten sites on the Grand River, Ontario, Canada. Gut contents were collected in fall 2018 from these fish at sites upstream and downstream of two municipal wastewater treatment plants (WWTPs; Waterloo and Kitchener). 16S rRNA genes were sequenced to determine the composition and diversity (alpha and beta) of microbial taxa present. Gut content bacterial alpha diversity increased downstream of both WWTP outfalls; dominance of bacterial amplicon sequence variants decreased compared to upstream fish. Fish collected at different sites had distinct bacterial communities, with upstream samples dominant in Proteobacteria and Firmicutes, and downstream samples increasingly abundant in Proteobacteria and Cyanobacteria. In mammals, increased abundance of Proteobacteria is indicative of microbial dysbiosis and has been linked to altered health outcomes, but this is not yet known for fish. This research indicates that the fish gut content microbiome was altered downstream of WWTP effluent outfalls and could lead to negative health outcomes.

Endobolome, a New Concept for Determining the Influence of Microbiota Disrupting Chemicals (MDC) in Relation to Specific Endocrine Pathogenesis

Endogenous steroid hormones and Endocrine Disrupting Chemicals (EDC) interact with gut microbiota through different pathways. We suggest the use of the term "endobolome" when referring to the group of gut microbiota genes and pathways involved in the metabolism of steroid hormones and EDC. States of dysbiosis and reduced diversity of the gut microbiota may impact and modify the endobolome resulting at long-term in the development of certain pathophysiological conditions. The endobolome might play a central role in the gut microbiota as seen by the amount of potentially endobolome-mediated diseases and thereby it can be considered an useful diagnostic tool and therapeutic target for future functional research strategies that envisage the use of next generation of probiotics. In addition, we propose that EDC and other xenobiotics that alter the gut microbial composition and its metabolic capacities should be categorized into a subgroup termed "microbiota disrupting chemicals" (MDC). This will help to distinguish the role of contaminants from other microbiota natural modifiers such as those contained or released from diet, environment, physical activity and stress. These MDC might have the ability to promote specific changes in the microbiota that can ultimately result in common intestinal and chronic or long-term systemic diseases in the host. The risk of developing certain disorders associated with gut microbiota changes should be established by determining both the effects of the MDC on gut microbiota and the impact of microbiota changes on chemicals metabolism and host susceptibility. In any case, further animal controlled experiments, clinical trials and large epidemiological studies are required in order to establish the concatenated impact of the MDC-microbiota-host health axis.

Distinct microbial assemblages associated with genetic selection for high- and low- muscle yield in rainbow trout

Background

Fish gut microbial assemblages play a crucial role in the growth rate, metabolism, and immunity of the host. We hypothesized that the gut microbiota of rainbow trout was correlated with breeding program based genetic selection for muscle yield. To test this hypothesis, fecal samples from 19 fish representing an F2 high-muscle genetic line (ARS-FY-H) and 20 fish representing an F1 low-muscle yield genetic line (ARS-FY-L) were chosen for microbiota profiling using the 16S rRNA gene. Significant differences in microbial assemblages between these two genetic lines might represent the effect of host genetic selection in structuring the gut microbiota of the host.

Results

Tukey’s transformed inverse Simpson indices indicated that high muscle yield genetic line (ARS-FY-H) samples have higher microbial diversity compared to those of the low muscle yield genetic line (ARS-FY-L) (LMM, χ2(1) =14.11, p < 0.05). The fecal samples showed statistically distinct structure in microbial assemblages between the genetic lines (F_1,36 = 4.7, p < 0.05, R² = 11.9%). Functional profiling of bacterial operational taxonomic units predicted characteristic functional capabilities of the microbial communities in the high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic line samples.

Conclusion

The significant differences of the microbial assemblages between high (ARS-FY-H) and low (ARS-FY-L) muscle yield genetic lines indicate a possible effect of genetic selection on the microbial diversity of the host. The functional composition of taxa demonstrates a correlation between bacteria and improving the muscle accretion in the host, probably, by producing various metabolites and enzymes that might aid in digestion. Further research is required to elucidate the mechanisms involved in shaping the microbial community through host genetic selection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07204-7.

Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

BACKGROUND

The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish (Seriola lalandi) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery.

RESULTS

Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fish - an effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skin-associated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more 'normal' (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT.

CONCLUSION

As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.

Differential responses of gut microbiota of male and female fathead minnow (Pimephales promelas) to a short-term environmentally-relevant, aqueous exposure to benzo[a]pyrene

In addition to aiding in digestion of food and uptake of nutrients, microbiota in guts of vertebrates are responsible for regulating several beneficial functions, including development of an organism and maintaining homeostasis. However, little is known about effects of exposures to chemicals on structure and function of gut microbiota of fishes. To assess effects of exposure to polycyclic aromatic hydrocarbons (PAHs) on gut microbiota, male and female fathead minnows (Pimephales promelas) were exposed to environmentally-relevant concentrations of the legacy PAH benzo[a]pyrene (BaP) in water. Measured concentrations of BaP ranged from 2.3 × 10^-3 to 1.3 μg L^-1. The community of microbiota in the gut were assessed by use of 16S rRNA metagenetics. Exposure to environmentally-relevant aqueous concentrations of BaP did not alter expression levels of mRNA for cyp1a1, a "classic" biomarker of exposure to BaP, but resulted in shifts in relative compositions of gut microbiota in females rather than males. Results presented here illustrate that in addition to effects on more well-studied molecular endpoints, relative compositions of the microbiota in guts of fish can also quickly respond to exposure to chemicals, which can provide additional mechanisms for adverse effects on individuals.

Antibiotic effect and microbiome persistence vary along the European seabass gut

The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat diseases, with adverse implications on the environment, animal health and commensal microbes. Gut microbes are important for the host proper functioning, thus evaluating such impacts is highly crucial. Examining the antibiotic impact on gut segments with different physiological roles may provide insight into their effects on these microhabitats. Hence, we evaluated the effect of feed-administrated antibiotics on the composition and metabolic potential of the gut microbiome in the European seabass, an economically important aquaculture species. We used quantitative PCR to measure bacterial copy numbers, and amplicon sequencing of the 16S rRNA gene to describe the composition along the gut, after 7-days administration of two broad-range antibiotic mixtures at two concentrations. While positive correlation was found between antibiotic concentration and bacterial abundance, we showed a differential effect of antibiotics on the composition along the gut, highlighting distinct impacts on these microbial niches. Moreover, we found an increase in abundance of predicted pathways related to antibiotic-resistance. Overall, we show that a high portion of the European seabass gut microbiome persisted, despite the examined antibiotic intake, indicating high stability to perturbations.

Phaeobacter inhibens controls bacterial community assembly on a marine diatom

Bacterial communities can have an important influence on the function of their eukaryotic hosts. However, how microbiomes are formed and the influence that specific bacteria have in shaping these communities is not well understood. Here, we used the marine diatom Thalassiosira rotula and the algal associated bacterium Phaeobacter inhibens as a model system to explore these questions. We exposed axenic (bacterial-free) T. rotula cultures to bacterial communities from natural seawater in the presence or absence of P. inhibens strain 2.10 or a variant strain (designated NCV12a1) that lacks antibacterial activity. We found that after 2 days the bacterial communities that assembled on the host were distinct from the free-living communities and comprised predominately of members of the Proteobacteria, Bacteroidetes and Cyanobacteria. In the presence of P. inhibens a higher abundance of Alphaproteobacteria, Flavobacteriia and Verrucomicrobia was detected. We also found only minor differences between the communities that established in the presence of either the wild type or the variant P. inhibens strain, suggesting that the antibacterial activity of P. inhibens is not the primary cause of its influence on bacterial community assembly. This study highlights the dynamic nature of algal microbiome development and the strong influence individual bacterial strains can have on this process.

Endocrine Disruptors in Food: Impact on Gut Microbiota and Metabolic Diseases

Endocrine disruptors (EDCs) have been associated with the increased incidence of metabolic disorders. In this work, we conducted a systematic review of the literature in order to identify the current knowledge of the interactions between EDCs in food, the gut microbiota, and metabolic disorders in order to shed light on this complex triad. Exposure to EDCs induces a series of changes including microbial dysbiosis and the induction of xenobiotic pathways and associated genes, enzymes, and metabolites involved in EDC metabolism. The products and by-products released following the microbial metabolism of EDCs can be taken up by the host; therefore, changes in the composition of the microbiota and in the production of microbial metabolites could have a major impact on host metabolism and the development of diseases. The remediation of EDC-induced changes in the gut microbiota might represent an alternative course for the treatment and prevention of metabolic diseases.

Toxicity evaluation and microbiota response of the lined sole Achirus lineatus (Chordata: Achiridae) exposed to the light petroleum water-accommodated fraction (WAF)

Exposure to contaminants might directly affect organisms and alter their associated microbiota. The objective of the present study was to determine the impact of the petroleum-water-accommodated fraction (WAF) from a light crude oil (API gravity 35) on a benthic fish species native from the Gulf of Mexico (GoM). Ten adults of Achirus lineatus (Linnaeus, 1758) were exposed to a sublethal WAF/water solution of 50% v/v for 48 hr. Multiple endpoints were measured including tissue damage, presence of polycyclic aromatic hydrocarbons (PAHs) metabolites in bile and gut microbiota analyses. Atrophy and fatty degeneration were observed in livers. Nodules and inflammation were detected in spleen, and structural disintegration and atrophy in the kidney. In gills hyperplasia, aneurysm, and gills lamellar fusion were observed. PAHs metabolites concentrations in bile were significantly higher in exposed organisms. Gut microbiome taxonomic analysis showed significant shifts in bacterial structure and composition following WAF exposure. Data indicate that exposure to WAF produced toxic effects in adults of A. lineatus, as evidenced by histological alterations and dysbiosis, which might represent an impairment to long-term subsistence of exposed aquatic organisms.

Gut Microbiome Toxicity: Connecting the Environment and Gut Microbiome-Associated Diseases

The human gut microbiome can be easily disturbed upon exposure to a range of toxic environmental agents. Environmentally induced perturbation in the gut microbiome is strongly associated with human disease risk. Functional gut microbiome alterations that may adversely influence human health is an increasingly appreciated mechanism by which environmental chemicals exert their toxic effects. In this review, we define the functional damage driven by environmental exposure in the gut microbiome as gut microbiome toxicity. The establishment of gut microbiome toxicity links the toxic effects of various environmental agents and microbiota-associated diseases, calling for more comprehensive toxicity evaluation with extended consideration of gut microbiome toxicity.

Perinatal Triclosan exposure in the rat induces long-term disturbances in metabolism and gut microbiota in adulthood and old age

Triclosan (TCS), as a widely used antimicrobial compound, is commonly detected in pregnant women and newborns indicating exposure risk during early development. However, whether perinatal TCS exposure has long-term effects on the host microbiome which further contributes to metabolic disorder is still unclear. The long-term effects of perinatal TCS exposure on gut microbiota and liver metabolism in adulthood and old age were investigated. Rats were given 0, 10 or 50 mg TCS/kg body weight per day, administered daily by gavage from gestation day 0 until lactation day 21. RNA-sequencing and 16 S rDNA amplicon sequencing analysis were performed to explore the potential mechanisms. Increased blood glucose and serum HDL-C were observed at 10 mg/kg/day in old rats and at 50 mg/kg/day in both adult and old rats. Serum leptin were increased at two doses in old rats. Serum TG and LDL-C were increased at two doses in both adult and old rats. Hepatic glycogen were decreased at 50 mg/kg/day in adult rats and at two doses in old rats. Increased hepatic TG were observed at two doses in old rats. Hepatic RNA-sequencing revealed that more differentially expressed genes were found at 50 mg/kg/day in both adult and old rats. More up-regulated genes in pathways of carbohydrate and lipid metabolism were observed in old rats at 50 mg/kg/day. Diversity reduction and compositional alteration were found in gut microbiota at 50 mg/kg/day in adult rats and at two doses in old rats. These effects lasted for a long time even without TCS exposure and accumulated over time inducing metabolic disorder in old rat offspring. TCS exposure during early life causes disturbances in metabolism and gut microbiota which last a lifetime and accumulated over time at 50 mg/kg/day. Further research is needed to investigate the effects of early life TCS exposure on metabolism and gut microbiota in humans.

Acute oral methylmercury exposure perturbs the gut microbiome and alters gut-brain axis related metabolites in rats

Environmental pollutants like methylmercury (MeHg) can bring devastating neurotoxicity to animals and human beings. Gut microbiota has been found to demethylate MeHg and promote the excretion of Hg through feces. However, the impacts of MeHg on gut microbiota and metabolites related to gut-brain interactions were less studied in mammals. The object of this study was to investigate the impacts of acute MeHg exposure on gut microbiome and metabolites together with its impact on gut integrity and related biological responses in rats. Rats were exposed to MeHg through oral administration and were sacrificed after 24 h 16 S rRNA gene sequencing was used to study the perturbance to gut microbiome and liquid chromatography mass spectrometry (LC-MS) was used for metabolomics profiling. It was found that gut was one of the target tissues of MeHg. MeHg induce the changes of intestinal microbial community structure and induce the regulating neuron activity change of intestinal neurotransmitters and metabolites on intestinal neurotransmitters and metabolites regulating the neuron activity. This was supported by the increased BDNF level. These findings may suggest a potential new mechanism regarding the neurotoxicity of MeHg. The protocols used in this study may also be applied to understand the neurotoxicity of other environmental neurotoxins like Pb, Mn, polychlorinated biphenyls, and pesticides, etc and to screen the neurotoxicity of emerging environmental contaminants.

Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations

BACKGROUND

The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensity, and gradient of disturbance, but also on the initial community structure, phylogenetic composition, legacy, and habitat (soil, water, host). In this study, yellow perch (Perca flavescens) juveniles were exposed over 90 days to constant and gradual sublethal doses of cadmium chloride. Afterward, the exposure of aquaria tank system to cadmium was ceased for 60 days. The skin, gut and water tank microbiomes in control and treatment groups, were characterized before, during and after the cadmium exposure using 16s rDNA libraries and high throughput sequencing technology (Illumina, Miseq).

RESULTS

Our data exhibited long-term bioaccumulation of cadmium salts in the liver even after two months since ceasing the exposure. The gradient of cadmium disturbance had differential effects on the perch microbiota recovery, including increases in evenness, taxonomic composition shifts, as well as functional and phylogenetic divergence. The perch microbiome reached an alternative stable state in the skin and nearly complete recovery trajectories in the gut communities. The recovery of skin communities showed a significant proliferation of opportunistic fish pathogens (i.e., Flavobacterium). Our findings provide evidence that neutral processes were a much more significant contributor to microbial community turnover in control treatments than in those treated with cadmium, suggesting the role of selective processes in driving community recovery.

CONCLUSIONS

The short-term metallic disturbance of fish development has important long-term implications for host health. The recovery of microbial communities after metallic exposure depends on the magnitude of exposure (constant, gradual), and the nature of the ecological niche (water, skin, and gut). The skin and gut microbiota of fish exposed to constant concentrations of cadmium (CC) were closer to the control negative than those exposed to the gradual concentrations (CV). Overall, our results show that the microbial assembly during the community recovery were both orchestrated by neutral and deterministic processes. Video Abtract.

Arsenic disturbs the gut microbiome of individuals in a disadvantaged community in Nepal

Arsenic is ubiquitous in nature, highly toxic, and is particularly abundant in Southern Asia. While many studies have focused on areas like Bangladesh and West Bengal, India, disadvantaged regions within Nepal have also suffered from arsenic contamination levels, with wells and other water sources possessing arsenic contamination over the recommended WHO and EPA limit of 10 μg/L, some wells reporting levels as high as 500 μg/L. Despite the region's pronounced arsenic concentrations within community water sources, few investigations have been conducted to understand the impact of arsenic contamination on host gut microbiota health. This study aims to examine differential arsenic exposure on the gut microbiome structure within two disadvantaged communities in southern Nepal. Fecal samples (n = 42) were collected from members of the Mahuawa (n = 20) and Ghanashyampur (n = 22) communities in southern Nepal. The 16S rRNA gene was amplified from fecal samples using Illumina-tag PCR and subject to high-throughput sequencing to generate the bacterial community structure of each sample. Bioinformatics analysis and multivariate statistics were conducted to identify if specific fecal bacterial assemblages and predicted functions were correlated with urine arsenic concentration. Our results revealed unique assemblages of arsenic volatilizing and pathogenic bacteria positively correlated with increased arsenic concentration in individuals within the two respective communities. Additionally, we observed that commensal gut bacteria negatively correlated with increased arsenic concentration in the two respective communities. Our study has revealed that arsenic poses a broader human health risk than was previously known. It is influential in shaping the gut microbiome through its enrichment of arsenic volatilizing and pathogenic bacteria and subsequent depletion of gut commensals. This aspect of arsenic has the potential to debilitate healthy humans by contributing to disorders like heart and liver cancers and diabetes, and it has already been shown to contribute to serious diseases and disorders, including skin lesions, gangrene and several types of skin, renal, lung, and liver cancers in disadvantaged areas of the world like Nepal.

Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax)

The mucosal surfaces of fish harbour microbial communities that can act as the first-line of defense against pathogens. Infectious diseases are one of the main constraints to aquaculture growth leading to huge economic losses. Despite their negative impacts on microbial diversity and overall fish health, antibiotics are still the method of choice to treat many such diseases. Here, we use 16 rRNA V4 metataxonomics to study over a 6 week period the dynamics of the gill and skin microbiomes of farmed seabass before, during and after a natural disease outbreak and subsequent antibiotic treatment with oxytetracycline. Photobacterium damselae was identified as the most probable causative agent of disease. Both infection and antibiotic treatment caused significant, although asymmetrical, changes in the microbiome composition of the gills and skin. The most dramatic changes in microbial taxonomic abundance occurred between healthy and diseased fish. Disease led to a decrease in the bacterial core diversity in the skin, whereas in the gills there was both an increase and a shift in core diversity. Oxytetracycline caused a decrease in core diversity in the gill and an increase in the skin. Severe loss of core diversity in fish mucosae demonstrates the disruptive impact of disease and antibiotic treatment on the microbial communities of healthy fish.

The Impact of Early-Life Exposure to Antimicrobials on Asthma and Eczema Risk in Children

PURPOSE OF REVIEW

We examined recent research on associations of prenatal and early-childhood exposure to the antimicrobial compounds, triclosan, and parabens, with the risk of asthma and eczema in children. We will discuss potential biological mechanisms of this association and highlight strengths and limitations of the study design and exposure assessment of current findings.

RECENT FINDINGS

Results of available toxicological and epidemiologic studies indicate a potential link of triclosan and paraben exposures with asthma and eczema in children, as well as changes in microbiome diversity and immune dysfunction, which could possibly mediate an association with the health outcomes. A small number of studies suggest that triclosan and paraben exposures could be related to the risk of asthma and eczema in children. Although current findings are far from conclusive, there is emerging evidence that changes in microbiome diversity and immune function from antimicrobial exposure may mediate these relations.

Triclosan-Selected Host-Associated Microbiota Perform Xenobiotic Biotransformations in Larval Zebrafish

Microbiota regulate important physiologic processes during early host development. They also biotransform xenobiotics and serve as key intermediaries for chemical exposure. Antimicrobial agents in the environment may disrupt these complex interactions and alter key metabolic functions provided by host-associated microbiota. To examine the role of microbiota in xenobiotic metabolism, we exposed zebrafish larvae to the antimicrobial agent triclosan. Conventionally colonized (CC), microbe-free axenic (AX), or axenic colonized on day 1 (AC1) zebrafish were exposed to 0.16-0.30 µM triclosan or vehicle on days 1, 6, 7, 8, and 9 days post fertilization (dpf). After 6 and 10 dpf, host-associated microbial community structure and putative function were assessed by 16S rRNA gene sequencing. At 10 dpf, triclosan exposure selected for bacterial taxa, including Rheinheimera. Triclosan-selected microbes were predicted to be enriched in pathways related to mechanisms of antibiotic resistance, sulfonation, oxidative stress, and drug metabolism. Furthermore, at 10 dpf, colonized zebrafish contained 2.5-3 times more triclosan relative to AX larvae. Nontargeted chemical analysis revealed that, relative to AX larvae, both cohorts of colonized larvae showed elevations in 23 chemical features, including parent triclosan and putative triclosan sulfate. Taken together, these data suggest that triclosan exposure selects for microbes that harbor the capacity to biotransform triclosan into chemical metabolites with unknown toxicity profiles. More broadly, these data support the concept that microbiota modify the toxicokinetics of xenobiotic exposure.

A common antimicrobial additive increases colonic inflammation and colitis-associated colon tumorigenesis in mice

Triclosan (TCS) is a high-volume chemical used as an antimicrobial ingredient in more than 2000 consumer products, such as toothpaste, cosmetics, kitchenware, and toys. We report that brief exposure to TCS, at relatively low doses, causes low-grade colonic inflammation, increases colitis, and exacerbates colitis-associated colon cancer in mice. Exposure to TCS alters gut microbiota in mice, and its proinflammatory effect is attenuated in germ-free mice. In addition, TCS treatment increases activation of Toll-like receptor 4 (TLR4) signaling in vivo and fails to promote colitis in Tlr4^-/- mice. Together, our results demonstrate that this widely used antimicrobial ingredient could have adverse effects on colonic inflammation and associated colon tumorigenesis through modulation of the gut microbiota and TLR4 signaling. Together, these results highlight the need to reassess the effects of TCS on human health and potentially update policies regulating the use of this widely used antimicrobial.

Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis thaliana Under Drought Stress

The rhizosphere is colonized by a mass of microbes, including bacteria capable of promoting plant growth that carry out complex interactions. Here, by using a sterile experimental system, we demonstrate that Sphingomonas sp. Cra20 promotes the growth of Arabidopsis thaliana by driving developmental plasticity in the roots, thus stimulating the growth of lateral roots and root hairs. By investigating the growth dynamics of A. thaliana in soil with different water-content, we demonstrate that Cra20 increases the growth rate of plants, but does not change the time of reproductive transition under well-water condition. The results further show that the application of Cra20 changes the rhizosphere indigenous bacterial community, which may be due to the change in root structure. Our findings provide new insights into the complex mechanisms of plant and bacterial interactions. The ability to promote the growth of plants under water-deficit can contribute to the development of sustainable agriculture.

Triclosan Alters Microbial Communities in Freshwater Microcosms

The effect of triclosan on microbial communities that are found in soil and sediments is well documented. However, little is known regarding the possible effects of triclosan on microbial communities that are present in the column of freshwater streams as the antimicrobial is released from sediments or from water sewage outflow. We show that a concentration of triclosan as low as 1 ng/L decreases richness and evenness in freshwater microbial communities growing in the water column while using controlled experimental microcosms. Crucially, the decrease in evenness that was observed in the microbial communities was due to the selection of bacteria commonly associated with human activity, such as Acinetobacter, Pseudomonas, and Rhodobacter, as opposed to an increase in Cyanobacteria, as previously suggested. Finally, our results demonstrate that higher concentrations of triclosan comparable to heavily polluted environments can also impact the overall phylogenetic structure and community composition of microbial communities. Understanding the impact of triclosan on these microbial populations is crucial from a public health perspective as human populations are more often exposed to microbial communities that are present in the water column via recreative use.

Gut microbiota of aquatic organisms: A key endpoint for ecotoxicological studies

Gut microbial communities constitute a compartment of crucial importance in regulation of homeostasis of multiple host physiological functions as well as in resistance towards environmental pollutants. Many chemical contaminants were shown to constitute a major threat for gut bacteria. Changes in gut microbiome could lead to alteration of host health. The access to high-throughput sequencing platforms permitted a great expansion of this discipline in human health while data from ecotoxicological studies are scarce and particularly those related to aquatic pollution. The main purpose of this review is to summarize recent body of literature providing data obtained from microbial community surveys using high-throughput 16S rRNA sequencing technology applied to aquatic ecotoxicity. Effects of pesticides, PCBs, PBDEs, heavy metals, nanoparticles, PPCPs, microplastics and endocrine disruptors on gut microbial communities are presented and discussed. We pointed out difficulties and limits provided by actual methodologies. We also proposed ways to improve understanding of links between changes in gut bacterial communities and host fitness loss, along with further applications for this emerging discipline.

The cervical microbiota in reproductive-age South African women with and without human papillomavirus infection

In this study we examined potential associations of HPV infection with the cervical microbiota. Cervical samples were collected from 87 HIV-seronegative reproductive-age Black South African women. Microbiota were characterized by Illumina sequencing of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. Thirty seven (42.5%) and 30 (34.5%) of the women had prevalent HPV and high-risk (HR)-HPV, respectively. Only 23 women (26.4%) had cervical microbiota dominated by a single Lactobacillus species (L. crispatus (2/87 (2.3%)), L. jensenii (2/87 (2.3%)), and L. iners (19/87 (21.8%)). The majority of the women (56/87 (64.4%)) had diverse cervical microbiota consisting of mainly bacterial vaginosis-associated bacteria. The remaining women (8/87 (9.2%)) had microbiota dominated by Aerococcus, Streptococcus, Chlamydia or Corynebacterium. Women with HR-HPV had significantly higher relative abundances of Aerococcaceae, Pseudomonadaceae and Bifidobacteriaceae compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05, q < 0.2). Gardnerella, Sneathia, and Atopobium were also found at greater relative abundances in HR-HPV-infected women compared to those with low-risk (LR)-HPV or no HPV-infection (LDA score >2.0, p < 0.05), although the difference was not significant after FDR-adjustment (q > 0.2). Further investigations of the bacterial taxa significantly enriched in HR-HPV-infected women are warranted.

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Majority of participants (74%) had cervical microbiota not dominated by Lactobacillus.

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Lactobacillus was not enriched in HPV-negative women compared to HPV-positive women.

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There was no correlation between cervical microbiota diversity and HPV infection.

Influences of dietary selenomethionine exposure on tissue accumulation, blood biochemical profiles, gene expression and intestinal microbiota of Carassius auratus

A 30-days feeding trail was conducted to determine the sensitivity of Carassius auratus to the toxicological effects of elevated dietary Selenomethionine (Se-Met). C. auratus averaging 23.56 ± 1.82 g were exposed to four Se-Met concentrations (mg Se/kg): 0 (Se-Met0), 5 (Se-Met5), 10 (Se-Met10) and 20 (Se-Met20) to estimate the effects on tissue selenium (Se) accumulation, blood biochemical profiles, transcript expression and intestinal microbiota. Se accumulated in the kidney, liver and muscle in a dose-dependent manner and followed this order: kidney > liver > muscle, the highest accumulation were obtained in kidney of Se-Met20 diet after 30 days of feeding. Serum contents of alanine transaminase (ALT), aspartate transaminase (AST) and alkaline phosphatase (ALP) in fish exposed to Se-Met20 group was significantly highest among Se-Met exposure groups. Hydrogen peroxide (H₂O₂) concentrations in liver were affected by dietary Se-Met exposures. Liver contents of total antioxidant capacity (TAC), catalase (CAT), glutathione peroxidase (GPx) and malondialdehyde (MDA) in fish exposure to Se-Met5 group was significantly highest among Se-Met exposure groups. Growth hormone receptor (GHR), insulin-like growth factor 1 (IGF-1) and antioxidant enzyme related genes including glutathione peroxidase (GPx), catalase (CAT) and glutathione S-transferase (GST) expression in liver were down-regulated with the concentration of Se-Met exposure groups. The results of high-throughput sequencing showed that gut microbial communities and hierarchy cluster heatmap analysis were significantly affected by Se-Met exposure. The abundances of Cetobacterium and Vibrio increased while fish exposed to Se-Met20 group. The abundance of Ralstonia increased when the Se-Met exposure dose reached 10 mg Se kg^-1. The results suggested that the exposure to elevated dietary Se-Met may result toxic effects in C. auratus.

The intestinal environment as an evolutionary adaptation to mouthbrooding in the Astatotilapia burtoni cichlid

Many of the various parental care strategies displayed by animals are accompanied by a significant reduction in food intake that imposes a substantial energy trade-off. Mouthbrooding, as seen in several species of fish in which the parent holds the developing eggs and fry in the buccal cavity, represents an extreme example of reduced food intake during parental investment and is accompanied by a range of physiological adaptations. In this study we use 16S sequencing to characterize the gut microbiota of female Astatotilapia burtoni cichlid fish throughout the obligatory phase of self-induced starvation during the brooding cycle in comparison to stage-matched females that have been denied food for the same duration. In addition to a reduction of gut epithelial turnover, we find a dramatic reduction in species diversity in brooding stages that recovers upon release of fry and refeeding that is not seen in females that are simply starved. Based on overall species diversity as well as differential abundance of specific bacterial taxa, we suggest that rather than reflecting a simple deprivation of caloric intake, the gut microbiota is more strongly influenced by physiological changes specific to mouthbrooding including the reduced epithelial turnover and possible production of antimicrobial agents.

Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month

BACKGROUND

Early disruption of the microbial community may influence life-long health. Environmental toxicants can contaminate breast milk and the developing infant gut microbiome is directly exposed. We investigated whether environmental toxicants in breastmilk affect the composition and function of the infant gut microbiome at 1 month. We measured environmental toxicants in breastmilk, fecal short-chain fatty acids (SCFAs), and gut microbial composition from 16S rRNA gene amplicon sequencing using samples from 267 mother-child pairs in the Norwegian Microbiota Cohort (NoMIC). We tested 28 chemical exposures: polychlorinated biphenyls (PCBs), polybrominated flame retardants (PBDEs), per- and polyfluoroalkyl substances (PFASs), and organochlorine pesticides. We assessed chemical exposure and alpha diversity/SCFAs using elastic net regression modeling and generalized linear models, adjusting for confounders, and variation in beta diversity (UniFrac), taxa abundance (ANCOM), and predicted metagenomes (PiCRUSt) in low, medium, and high exposed groups.

RESULTS

PBDE-28 and the surfactant perfluorooctanesulfonic acid (PFOS) were associated with less microbiome diversity. Some sub-OTUs of Lactobacillus, an important genus in early life, were lower in abundance in samples from infants with relative "high" (> 80th percentile) vs. "low" (< 20th percentile) toxicant exposure in this cohort. Moreover, breast milk toxicants were associated with microbiome functionality, explaining up to 34% of variance in acetic and propionic SCFAs, essential signaling molecules. Per one standard deviation of exposure, PBDE-28 was associated with less propionic acid (- 24% [95% CI - 35% to - 14%] relative to the mean), and PCB-209 with less acetic acid (- 15% [95% CI - 29% to - 0.4%]). Conversely, PFOA and dioxin-like PCB-167 were associated with 61% (95% CI 35% to 87%) and 22% (95% CI 8% to 35%) more propionic and acetic acid, respectively.

CONCLUSIONS

Environmental toxicant exposure may influence infant gut microbial function during a critical developmental window. Future studies are needed to replicate these novel findings and investigate whether this has any impact on child health.

Dietary Lactobacillus plantarum ST-III alleviates the toxic effects of triclosan on zebrafish (Danio rerio) via gut microbiota modulation

The probiotics, Lactobacillus plantarum ST-III, plays an important role in modulating microbiota and alleviating intestinal metabolic disorders. Herein, we reported that Lactobacillus increases biodiversity of zebrafish gut flora, and attenuates toxic effects from chronic triclosan (TCS) exposure. Lactobacillus-feeding recovered the species and amount of microorganisms in the intestines of zebrafish, and inhibited toxin production by saprophytic bacterial growth. Abnormal physiological indexes and malonaldeyhde content resulting from TCS exposure were effectively alleviated. Additionally, lipid-metabolism disorders, such as increased triglyceride and total cholesterol levels, were attenuated by a probiotics diet. The number of CD4⁺ T cell lymphocytes in the lamina propria of the duodenal mucosa was decreased in zebrafish receiving a Lactobacillus diet compared to the TCS-exposed group, showing a consistent expression trend for six immune genes (NF-κB, IL-1β, TNF-α, lysozyme, TLR4α, IL-10) in the intestinal mucosa. Histopathological observations of intestines, spleen and kidney showed that TCS exposure produced severe damage to the morphology and structure of immune and metabolism-related organs. Lactobacillus was capable of mitigating this damage, but bile salt hydrolase, an active extract of Lactobacillus, was not an effective mitigation strategy. The Lactobacillus-induced decrease in the number of inflammatory cells confirmed its role in preventing inflammatory injury. Three behavioral tests (T-maze, bottom dwelling and social interaction) indicated that a probiotics diet improved zebrafish movement and learning/memory capacity, effectively alleviating anxiety behavior due to TCS exposure. These findings inform development of beneficial strategies to alleviate intestinal metabolic syndromes and neurodegenerative diseases resulting from exposure to environmental contaminants through modifying gut flora with a probiotics diet.

Oral administration of Lactobacillus plantarum attenuates inflammatory damage in mice challenged with two pathogens

This study aimed to determine the immunomodulatory effect of Lactobacillus plantarum on Salmonella typhimurium and Staphylococcus aureus infection. A mouse inflammation model was established using S. aureus and S. typhimurium. The infected mice were treated with low, medium, and high doses (2 × 108, 4 × 108, and 8 × 108 colony forming units (CFU)/mL, respectively) of three antibacterial L. plantarum strains. The body weight changes, spleen and thymus indexes, cytokines (interleukin (IL)-4 and interferon (IFN)-γ), and secreted immunoglobulin A levels were measured. Compared with the model group, all the L. plantarum-treated groups show increased body weight, reduced spleen swelling, decreased IFN-γ content, significantly increased IL-4 content, and significantly decreased ratio of IFN-γ to IL-4. sIgA levels increased at the end of the experiment. The three L. plantarum strains can effectively attenuate the symptoms of S. typhimurium and S. aureus infection by regulating the Th1/Th2 response and enhancing sIgA secretion.

Triclosan, a common antimicrobial ingredient, on gut microbiota and gut health

Triclosan (TCS) is an antimicrobial compound incorporated into more than 2,000 consumer products. This compound is frequently detected in the human body and causes ubiquitous contamination in the environment, raising concerns about its impact on human health and environmental pollution. Our recent research showed that exposure to TCS exaggerates colonic inflammation and exacerbates development of colitis-associated colon tumorigenesis, via gut microbiome-dependent mechanisms. In this review, we discussed recent research about TCS, as well as other consumer antimicrobials, on the gut microbiome and gut health.

Consumer Antimicrobials on Gut Microbiota and Gut Health

Triclosan (TCS) is a high-volume chemical used as an antimicrobial ingredient in over 2000 consumer products such as toothpastes, cosmetics, and toys. Due to its widespread use, it causes ubiquitous contamination in the environment and is frequently detected in the human body, raising concerns about its impact on environmental pollution and human health. Our recent study showed that short-time exposure to low-dose TCS causes colonic inflammation, increases severity of colitis, and exacerbates colitis-associated colon tumorigenesis in mice, through gut microbiota- and Toll-like receptor 4 (TLR4)-dependent mechanisms. In addition, we demonstrate that beyond TCS, other antimicrobial chemicals used in consumer products also exaggerate colitis and colon cancer in mice. Together, these results highlight the importance to further evaluate these consumer antimicrobials on gut health, to develop potential further regulatory policies.

The gut microbiome and aquatic toxicology: An emerging concept for environmental health

The microbiome plays an essential role in the health and onset of diseases in all animals, including humans. The microbiome has emerged as a central theme in environmental toxicology because microbes interact with the host immune system in addition to its role in chemical detoxification. Pathophysiological changes in the gastrointestinal tissue caused by ingested chemicals and metabolites generated from microbial biodegradation can lead to systemic adverse effects. The present critical review dissects what we know about the impacts of environmental contaminants on the microbiome of aquatic species, with special emphasis on the gut microbiome. We highlight some of the known major gut epithelium proteins in vertebrate hosts that are targets for chemical perturbation, proteins that also directly cross-talk with the microbiome. These proteins may act as molecular initiators for altered gut function, and we propose a general framework for an adverse outcome pathway that considers gut dysbiosis as a major contributing factor to adverse apical endpoints. We present 2 case studies, nanomaterials and hydrocarbons, with special emphasis on the Deepwater Horizon oil spill, to illustrate how investigations into the microbiome can improve understanding of adverse outcomes. Lastly, we present strategies to functionally relate chemical-induced gut dysbiosis with adverse outcomes because this is required to demonstrate cause-effect relationships. Further investigations into the toxicant-microbiome relationship may prove to be a major breakthrough for improving animal and human health. Environ Toxicol Chem 2018;37:2758-2775. © 2018 SETAC.

Dysbiosis and early mortality in zebrafish larvae exposed to subclinical concentrations of streptomycin

Exposure to low concentrations of antibiotics found in aquatic environments can increase susceptibility to infection in adult fish due to microbiome disruption. However, little is known regarding the effect of antibiotic pollution on fish larvae. Here, we show that exposure to streptomycin, a common antibiotic used in medicine and aquaculture, disrupts the normal composition of zebrafish larvae microbiomes, significantly reducing the microbial diversity found in the fish. Exposure to streptomycin also significantly increased early mortality among fish larvae, causing full mortality within a few days of exposure at 10 μg/mL. Finally, we found that subclinical concentrations of streptomycin also increased the abundance of class 1 integrons, an integrase-dependent genetic system associated to the horizontal transfer of antibiotic resistance genes, in the larvae microbiomes. These results suggest that even low concentrations of streptomycin associated with environmental pollution could impact fish populations and lead to the creation of antibiotic resistance reservoirs.

Fish Gut Microbiome: Current Approaches and Future Perspectives

In recent years, investigations of microbial flora associated with fish gut have deepened our knowledge of the complex interactions occurring between microbes and host fish. The gut microbiome not only reinforces the digestive and immune systems in fish but is itself shaped by several host-associated factors. Unfortunately, in the past, majority of studies have focused upon the structure of fish gut microbiome providing little knowledge of effects of these factors distinctively and the immense functional potential of the gut microbiome. In this review, we have highlighted the recently gained insights into the diversity and functions of the fish gut microbiome. We have also delved on the current approaches that are being employed to study the fish gut microbiome with an aim to collate all the knowledge gained and make accurate conclusions for their application based perspectives. The literature reviewed indicated that the future research should shift towards functional microbiomics to improve the maximum sustainable yield in aquaculture.

Alterations to the Intestinal Microbiome and Metabolome of Pimephales promelas and Mus musculus Following Exposure to Dietary Methylmercury

Mercury is a global contaminant, which may be microbially transformed into methylmercury (MeHg), which bioaccumulates. This results in potentially toxic body burdens in high trophic level organisms in aquatic ecosystems and maternal transfer to offspring. We previously demonstrated effects on developing fish including hyperactivity, altered time-to-hatch, reduced survival, and dysregulation of the dopaminergic system. A link between gut microbiota and central nervous system function in teleosts has been established with implications for behavior. We sequenced gut microbiomes of fathead minnows exposed to dietary MeHg to determine microbiome effects. Dietary exposures were repeated with adult CD-1 mice. Metabolomics was used to screen for metabolome changes in mouse brain and larval fish, and results indicate effects on lipid metabolism and neurotransmission, supported by microbiome data. Findings suggest environmentally relevant exposure scenarios may cause xenobiotic-mediated dysbiosis of the gut microbiome, contributing to neurotoxicity. Furthermore, small-bodied teleosts may be a useful model species for studying certain types of neurodegenerative diseases, in lieu of higher vertebrates.

Household triclosan and triclocarban effects on the infant and maternal microbiome

In 2016, the US Food and Drug Administration banned the use of specific microbicides in some household and personal wash products due to concerns that these chemicals might induce antibiotic resistance or disrupt human microbial communities. Triclosan and triclocarban (referred to as TCs) are the most common antimicrobials in household and personal care products, but the extent to which TC exposure perturbs microbial communities in humans, particularly during infant development, was unknown. We conducted a randomized intervention of TC‐containing household and personal care products during the first year following birth to characterize whether TC exposure from wash products perturbs microbial communities in mothers and their infants. Longitudinal survey of the gut microbiota using 16S ribosomal RNA amplicon sequencing showed that TC exposure from wash products did not induce global reconstruction or loss of microbial diversity of either infant or maternal gut microbiotas. Broadly antibiotic‐resistant species from the phylum Proteobacteria, however, were enriched in stool samples from mothers in TC households after the introduction of triclosan‐containing toothpaste. When compared by urinary triclosan level, agnostic to treatment arm, infants with higher triclosan levels also showed an enrichment of Proteobacteria species. Despite the minimal effects of TC exposure from wash products on the gut microbial community of infants and adults, detected taxonomic differences highlight the need for consumer safety testing of antimicrobial self‐care products on the human microbiome and on antibiotic resistance.

Effects of triclosan in breast milk on the infant fecal microbiome

Triclosan is frequently used for its antimicrobial properties and has been detected in human serum, urine, and breast milk. Animal and molecular studies have shown that triclosan exerts a wide range of adverse health effects at both high (ppm) and low (ppb) concentrations. Since triclosan is of growing concern to human and environmental health, there is a need to improve extraction procedures and to study additional effects from triclosan exposure. In this study, we have improved triclosan extraction from breast milk by using salt (MgSO4) to reduce emulsion formation and increase water polarity and water (∼80%) to enhance the overall extraction efficiency (∼3.5 fold). This extraction method was applied to breast milk samples collected from donors who i) recorded their use of triclosan-containing personal care products and ii) provided matching infant stool samples. Of the participants who had detectable amounts of triclosan in their breast milk, nine (75%) of them reported daily use of triclosan-containing personal care products. Levels of triclosan in breast milk were compared to the donor's infant's fecal microbiome. We found that the bacterial diversity in the fecal microbiome of the infants exposed to breast milk with detectable triclosan levels differed compared to their peers exposed to milk containing non-detectable amounts. This finding implies that exogenous chemicals are impacting microbiome diversity.

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish

Exposure to environmental toxins such as heavy metals can perturb the development and stability of microbial communities associated with human or animal hosts. Widespread arsenic contamination in rivers and riparian habitats therefore presents environmental and health concerns for populations living near sources of contamination. To investigate how arsenic affects host microbiomes, we sequenced and characterized the microbiomes of twenty larval zebrafish exposed to three concentrations of arsenic that are found in contaminated water—low (10 ppb), medium (50 ppb), and high (100 ppb) for 20 days. We found that even a small concentration of arsenic changed the overall microbial composition, structure and diversity of microbial communities, causing dysbiosis in developing larval zebrafish microbiota. In addition, we found that a high concentration of arsenic also increased the abundance of a class 1 integron, an integrase-dependent system facilitating the horizontal transfer of genes conferring resistance to heavy metals and antibiotics.

Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi

This study examined the technical bias associated with different DNA extraction methods used in microbiome research. Three methods were used to extract genomic DNA from the same intestinal microbiota sample that was taken from the koi carp Cyprinus carpio var. koi, after which their microbial diversity and community structure were investigated on the basis of a 16S rDNA high‐throughput sequencing analysis. Biased results were observed in relation to the number of reads, alpha diversity indexes and taxonomic composition among the three DNA extraction protocols. A total of 1,381 OTUs from the intestinal bacteria were obtained, with 852, 759, and 698 OTUs acquired, using the Lysozyme and Ultrasonic Lysis method, Zirmil‐beating Cell Disruption method, and a QIAamp Fast DNA Stool Mini Kit, respectively. Additionally, 336 OTUs were commonly acquired, using the three methods. The results showed that the alpha diversity indexes (Rarefaction, Shannon, and Chao1) of the community that were determined using the Lysozyme and Ultrasonic Lysis method were higher than those obtained with the Zirmil‐beating Cell Disruption method, while the Zirmil method results were higher than those measured, using the QIAamp Fast DNA Stool Mini Kit. Moreover, all the major phyla (ratio>1%) could be identified with all three DNA extraction methods, but the phyla present at a lower abundance (ratio <1%) could not. Similar findings were observed at the genus level. Taken together, these findings indicated that the bias observed in the results about the community structure occurred primarily in OTUs with a lower abundance. The results of this study demonstrate that possible bias exists in community analyses, and researchers should therefore be conservative when drawing conclusions about community structures based on the currently available DNA extraction methods.

A modified method for genomic DNA extraction from the fish intestinal microflora

A modified genomic DNA extraction method named the combination of lysozyme and ultrasonic lysis (CLU) method was used to analyze the fish intestinal microflora. In this method, the physical disruption and chemical lysis steps were combined, and some parameters in the key steps were adjusted. In addition, the results obtained by this method were compared with the results obtained by the Zirmil-beating cell disruption method and the QIAamp Fast DNA Stool Mini Kit. The OD₂₆₀/OD₂₈₀ ratio and concentration of the DNA extracted using the CLU method were 2.02 and 282.8 µg/µL, respectively; when the incubation temperatures for lysozyme and RNase were adjusted to 37 °C, those values were 2.08 and 309.8 µg/µL, respectively. On the agarose gel, a major high-intensity, discrete band of more than 10 kb was found for the CLU method. However, the smearing intensity of degraded DNA was lower when the incubation temperatures were 60 °C for lysozyme and 30 °C for RNase than when incubation temperatures of 37 °C for lysozyme and 37 °C for RNase were used. The V3 variable region of the prokaryotic 16S rDNA was amplified, and an approximately 600-bp fragment was observed when the DNA extracted using the CLU method was used as a template. The CLU method is simple and cost effective, and it yields high-quality, unsheared, high-molecular-weight DNA, which is comparable to that obtained with a commercially available kit. The extracted DNA has potential for applications in critical molecular biology techniques.

Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp

Gut microbiota contributes positively to the physiology of their host. Some feed additives have been suggested to improve livestock health and stimulate growth performance by modulating gut bacteria species. Here, we fed grass carp with 0 (control), 8% (Treat1), 10% (Treat2), 12% (Treat3) and 16% (Treat4) of yeast culture (YC) for 10 weeks. The gut microbiota was analysed by 16S rRNA gene V3-4 region via an Illumina MiSeq platform. PCoA test showed that gut bacterial communities in the control and Treat3 formed distinctly separate clusters. Although all the groups shared a large size of OTUs as a core microbiota community, a strong distinction existed at genus level. Treat3 contained the highest proportion of the beneficial bacteria and obviously enhanced the capacity of amino acid, lipid metabolism and digestive system. In addition, Treat3 significantly improved the fish growth and increased the liver and serum T-SOD activities while dramatically decreased the liver GPT and GOT. Collectively, these findings demonstrate the beneficial effects of YC feeding on gut microbiota, growth and biochemical parameters and Treat3 might be the optimal supplementation amount for grass carp, which opens up the possibility that a new feed additive can be developed for healthy aquaculture.

Early life Triclosan exposure and child adiposity at 8 Years of age: a prospective cohort study

BACKGROUND

Triclosan is an antimicrobial agent that may affect the gut microbiome and endocrine system to influence adiposity. However, little data from prospective studies examining prenatal and childhood exposures exist. We investigated the relationship between multiple, prospective early life measure of triclosan exposure and child adiposity.  METHODS: In a prospective cohort of 220 mother-child pairs from Cincinnati, OH (enrolled 2003-2006), we quantified triclosan in urine samples collected twice during pregnancy, annually from 1 to 5 years of age, and once at 8 years. We assessed child adiposity at age 8 years using body mass index (BMI), waist circumference, and bioelectric impedance. We estimated covariate-adjusted associations of child adiposity with a 10-fold increase in average prenatal, average early childhood (average of 1-5 years), and 8-year triclosan concentrations.

RESULTS

Among all children, there was no association between triclosan and child adiposity. While urinary triclosan concentrations at all three time periods were weakly, imprecisely, and inversely associated with all three measures of adiposity among girls, these associations did not differ significantly from those in boys (sex x triclosan p-values> 0.35). Among girls, the strongest associations were generally observed for prenatal triclosan when we adjusted for all three triclosan concentrations and covariates in the same model; BMI z-score (β: -0.13; 95% CI: -0.42, 0.15), waist circumference (β: - 1.7 cm; 95% CI: -4.2, 0.7), and percent body fat (β :-0.6; 95% CI: -2.7, 1.3). In contrast, the associations between triclosan concentrations and adiposity measures were inconsistent among boys.

CONCLUSION

We did not observe evidence of an association of repeated urinary triclosan concentrations during pregnancy and childhood with measures of child adiposity at age 8 years in this cohort.

Longitudinal Analysis of Fecal Microbiome and Pathologic Processes in a Rotenone Induced Mice Model of Parkinson's Disease

Recent studies reported an association between gut microbiota composition and Parkinson’s disease (PD). However, we know little about the relationship between microbiome dysbiosis and the pathogenesis of PD. The objective of this study was to describe the evolution of fecal microbiota using an oral rotenone model of PD from a longitudinal study over a period of 4 weeks. Gastrointestinal function was assessed by measuring fecal pellet output, motor functions was assessed by open-field and pole tests every week. α-synuclein pathology, inflammation and tyrosine hydroxylase (TH) neuron loss from the middle brain were also analyzed. Fecal samples were collected every week followed by 16S rRNA sequencing and bioinformatics analysis. We reported that chronically oral administered rotenone caused gastrointestinal dysfunction and microbiome dysbiosis prior to motor dysfunction and central nervous system (CNS) pathology. 16S rRNA sequencing of fecal microbiome showed rotenone-treated mice exhibited fecal microbiota dysbiosis characterized by an overall decrease in bacterial diversity and a significant change of microbiota composition, notably members of the phyla Firmicutes and Bacteroidetes, with an increase in Firmicutes/Bacteroidetes ratio after 3 weeks of rotenone treatment. Moreover, rotenone-induced gastrointestinal and motor dysfunctions were observed to be robustly correlated with changes in the composition of fecal microbiota. Our results demonstrated that gut microbiome perturbation might contribute to rotenone toxicity in the initiation of PD and brought a new insight in the pathogenesis of PD. Novel therapeutic options aimed at modifying the gut microbiota composition might postpone the onset and following cascade of neurodegeneration.

Ammonia exposure alters the expression of immune-related and antioxidant enzymes-related genes and the gut microbial community of crucian carp (Carassius auratus)

Chronic exposure of ammonia in fish can affect the activities of antioxidant enzymes but few studies investigate the influence of ammonia exposure on the expression of immune-related and antioxidant enzymes-related genes. Also, there is no study demonstrates the effect of ammonia exposure on gut microbial community of fish. In this study, crucian carp (Carassius auratus) were exposed to the ammonia concentrations, 0 (control), 10 mg L^-1 (low) or 50 mg L^-1 (high) for consecutive 30 days at 25 ± 1 °C temperature, respectively, and after that, the fish from all exposure groups were maintained in control conditions for another 15 days. The results showed that low concentration ammonia increased the expression of immune-related genes and antioxidant enzymes-related genes, but high concentration ammonia inhibited the expression of immune-related genes and antioxidant enzymes-related genes. After a 15-day treatment without ammonia, the expression of antioxidant enzymes-related genes and immune-related genes showed no significant changes compared with control. The results of high-throughput sequencing showed that gut microbial communities were significantly differentiated following ammonia exposure. The abundance of Bacteroides and Cetobacterium (two kinds of potential probiotics) increased while fish exposed to 10 mg L^-1 ammonia. The Flavobacterium (a potential fish pathogen) showed increasing trends when the exposure dose reached 50 mg L^-1, while the Bacteroides and Cetobacterium showed almost no abundance. The results also revealed that ammonia exposure concentration or time can alter the intestinal microbial community. In conclusion, ammonia exposure could induce the immune response in crucian carp, and alter the gut microbial community. The results may help us understand the correlations of gut microbial community shift and ammonia exposure and extend our knowledge to comprehend the effects of environmental factors on intestinal microbial community.

Teleosts as Model Organisms To Understand Host-Microbe Interactions

Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis.

Hypothesis Testing and Statistical Analysis of Microbiome

After the initiation of Human Microbiome Project in 2008, various biostatistic and bioinformatic tools for data analysis and computational methods have been developed and applied to microbiome studies. In this review and perspective, we discuss the research and statistical hypotheses in gut microbiome studies, focusing on mechanistic concepts that underlie the complex relationships among host, microbiome, and environment. We review the current available statistic tools and highlight recent progress of newly developed statistical methods and models. Given the current challenges and limitations in biostatistic approaches and tools, we discuss the future direction in developing statistical methods and models for the microbiome studies.

Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes

Background

Environmental chemical-induced perturbations of gut microbiome are associated with a series of adverse health outcomes. The effects of triclosan on human health have been controversial in recent years. The purpose of this study is to investigate the functional impact of triclosan on the mouse gut microbiome and the link between triclosan exposure and resistomes in gut bacteria.

Methods

We combined 16S rRNA gene sequencing and shotgun metagenomics sequencing to examine the compositional and functional impact of triclosan exposure on the gut microbiota of C57BL/6 mice.

Results

16S rRNA sequencing results revealed that 13-week triclosan exposure in drinking water induced significant perturbations in mouse gut bacterial assemblages with distinct trajectories compared to controls. Metagenomics sequencing results indicated a remarkable enrichment of gut bacterial genes related to triclosan resistance, stress response, antibiotic resistance and heavy metal resistance.

Conclusions

Triclosan exposure has a profound impact on the mouse gut microbiome by inducing perturbations at both compositional and functional levels. To our best knowledge, this is the first evidence regarding the functional alterations of gut microbiome induced by triclosan exposure, which may provide novel mechanistic insights into triclosan exposure and associated diseases.

The effect of immunoregulation of Streptococcus lactis L16 strain upon Staphylococcus aureus infection

BACKGROUND

Staphylococcus aureus is an important pathogen that causes various infections in medical facilities. However, resistance to multiple drugs has made this infection difficult to manage. Thus, new therapeutic strategies are urgently needed to solve this worldwide public health problem. The Streptococcus lactis L16 strain was isolated from the fermented hot chili sauce. To explore whether it can be used as a protective agent against S. aureus infection, we designed a mouse model of S. aureus infection to evaluate the therapeutic potency of S. lactis. Mice were grouped into pre-(P) and post-(T) S. aureus infection groups following oral administration of S. lactis L16. The protection and treatment effects were assessed by examining body weight, internal organ weight, serum cytokines and intestinal secretory IgA alternations.

RESULT

Oral administration of the S. lactis L16 strain reduced the loss of body weight in mice post-infection and alleviated infection-induced hepatomegaly. In particular, the PL16 group (protection with L16) showed more effective resistance to S. aureus than the TL16 group (treatment with L16). The level of serum cytokine interferon gamma following oral administration of the L16 strain was remarkably increased during infection, as were interleukin-4 levels during convalescence. The probiotic L16 strain induced more sIgA production than S. aureus.

CONCLUSION

Our data suggest that S. lactis L16 is an effective strain with anti-Staphylococcus activity. By regulating the Th1/Th2 response, S. lactis can effectively reduce lesions from infection, indicating its therapeutic potential in overcoming antibiotic resistance in this mouse infection model that mimics infections observed in humans.

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics

The gut microbiome of vertebrates plays an integral role in host health by stimulating development of the immune system, aiding in nutrient acquisition and outcompeting opportunistic pathogens. Development of next-generation sequencing technologies allows researchers to survey complex communities of microorganisms within the microbiome at great depth with minimal costs, resulting in a surge of studies investigating bacterial diversity of fishes. Many of these studies have focused on the microbial structure of economically significant aquaculture species with the goal of manipulating the microbes to increase feed efficiency and decrease disease susceptibility. The unravelling of intricate host-microbe symbioses and identification of core microbiome functions is essential to our ability to use the benefits of a healthy microbiome to our advantage in fish culture, as well as gain deeper understanding of bacterial roles in vertebrate health. This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome.

Ecotoxicity of veterinary enrofloxacin and ciprofloxacin antibiotics on anuran amphibian larvae

The ecological risks posed by two β-diketone antibiotics (DKAs, enrofloxacin, ENR and ciprofloxacin, CPX), characterized by their long persistence in aqueous environments and known deleterious effect on model organisms such as zebrafish were analysed using Rhinella arenarum larvae. Sublethal tests were conducted using environmentally relevant concentrations of both ENR and CPX (1-1000μgL^-1) under standard laboratory conditions for 96h. Biological endpoints and biomarkers evaluated were body size, shape, development and growth rates, and antioxidant enzymes (glutathione-S-transferase, GST; Catalase, CAT). Risk assessment was analysed based on ration quotients (RQ). The size and shape measurements of the larvae exposed to concentrations greater than 10μgL^-1 of CPX were lower compared to controls (Dunnett post hoc p<0.05) and presented signs of emaciation. Concentrations of 1000μgL^-1of CPX induced GST activity, in contrast with inhibited GST and CAT of larvae exposed to ENR. Risk assessments indicated that concentrations greater than or equal to10μgL^-1 of CPX and ENR are ecotoxic for development, growth, detoxifying, and oxidative stress enzymes. It is suggested that additional risk assessments may provide evidence of bioaccumulation of CPX and ENR in tissues or organs of amphibian larvae by mesocosm sediment test conditions. Finally, intestinal microbiome studies should be considered to establish the mechanisms of action of both antibiotics.