Core Gut Microbiota Research Articles

Chronotropic and vasoactive properties of the gut bacterial short-chain fatty acids in larval zebrafish.

Short-chain fatty acids (SCFAs) produced by the gut bacteria have been associated with cardiovascular dysfunction in humans and rodents. However, studies exploring effects of SCFAs on cardiovascular parameters in the zebrafish, an increasingly popular model in cardiovascular research, remain limited. Here, we performed fecal bacterial 16S sequencing and gas chromatography/mass spectrometry (GC-MS) to determine the composition and abundance of gut microbiota and SCFAs in adult zebrafish. Following this, the acute effects of major SCFAs on heart rate and vascular tone were measured in anesthetized zebrafish larvae using fecal concentrations of butyrate, acetate, and propionate. Finally, we investigated if coincubation with butyrate may lessen the effects of angiotensin II (ANG II) and phenylephrine (PE) on vascular tone in anesthetized zebrafish larvae. We found that the abundance in Proteobacteria, Firmicutes, and Fusobacteria phyla in the adult zebrafish resembled those reported in rodents and humans. SCFA levels with highest concentration of acetate (27.43 µM), followed by butyrate (2.19 µM) and propionate (1.65 µM) were observed in the fecal samples of adult zebrafish. Immersion in butyrate and acetate produced a ∼20% decrease in heart rate (HR), respectively, with no observed effects of propionate. Butyrate alone also produced an ∼25% decrease in the cross-sectional width of the dorsal aorta (DA) at 60 min (*P < 0.05), suggesting compensatory vasoconstriction, with no effects of either acetate or propionate. In addition, butyrate significantly alleviated the decrease in DA cross-sectional width produced by both ANG II and PE. We demonstrate the potential for zebrafish in investigation of host-microbiota interactions in cardiovascular health.NEW & NOTEWORTHY We highlight the presence of a core gut microbiota and demonstrate in vivo short-chain fatty acid production in adult zebrafish. In addition, we show cardio-beneficial vasoactive and chronotropic properties of butyrate, and chronotropic properties of acetate in anesthetized zebrafish larvae.

Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease.

The escalation of urbanization correlates with rising rates of inflammatory bowel disease (IBD), necessitating research into new etiological factors. This study aims to elucidate the gut microbiota profiles in IBD patients and compare them with healthy controls in a western city of China. We conducted a multicenter case-control study from the end of 2020, using 16S rRNA gene sequencing (n = 36) and metagenomic sequencing (n = 12) to analyze the gut microbiota of newly diagnosed IBD patients, including those with Crohn's disease (CD) and ulcerative colitis (UC). Our results demonstrated a significant enrichment of the phylum Proteobacteria, particularly the genus Escherichia-Shigella, in CD patients. Conversely, the genus Enterococcus was markedly increased in UC patients. The core gut microbiota, such as the Christensenellaceae R-7 group, Fusicatenibacter, and Holdemanella, were primarily identified in healthy subjects. Additionally, significant interactions between the microbiome and virulence factors were observed. The findings suggest that oxidative stress may play a pivotal role in the pathology of IBD. This study contributes to the growing dialogue about the impact of gut microbiota on the development of IBD and its variations across different geographies, highlighting potential avenues for further research.

Gut microbiome features and metabolites in non-alcoholic fatty liver disease among community-dwelling middle-aged and older adults

BackgroundThe specific microbiota and associated metabolites linked to non-alcoholic fatty liver disease (NAFLD) are still controversial. Thus, we aimed to understand how the core gut microbiota and metabolites impact NAFLD.MethodsThe data for the discovery cohort were collected from the Guangzhou Nutrition and Health Study (GNHS) follow-up conducted between 2014 and 2018. We collected 272 metadata points from 1546 individuals. The metadata were input into four interpretable machine learning models to identify important gut microbiota associated with NAFLD. These models were subsequently applied to two validation cohorts [the internal validation cohort (n = 377), and the prospective validation cohort (n = 749)] to assess generalizability. We constructed an individual microbiome risk score (MRS) based on the identified gut microbiota and conducted animal faecal microbiome transplantation experiment using faecal samples from individuals with different levels of MRS to determine the relationship between MRS and NAFLD. Additionally, we conducted targeted metabolomic sequencing of faecal samples to analyse potential metabolites.ResultsAmong the four machine learning models used, the lightGBM algorithm achieved the best performance. A total of 12 taxa-related features of the microbiota were selected by the lightGBM algorithm and further used to calculate the MRS. Increased MRS was positively associated with the presence of NAFLD, with odds ratio (OR) of 1.86 (1.72, 2.02) per 1-unit increase in MRS. An elevated abundance of the faecal microbiota (f__veillonellaceae) was associated with increased NAFLD risk, whereas f__rikenellaceae, f__barnesiellaceae, and s__adolescentis were associated with a decreased presence of NAFLD. Higher levels of specific gut microbiota-derived metabolites of bile acids (taurocholic acid) might be positively associated with both a higher MRS and NAFLD risk. FMT in mice further confirmed a causal association between a higher MRS and the development of NAFLD.ConclusionsWe confirmed that an alteration in the composition of the core gut microbiota might be biologically relevant to NAFLD development. Our work demonstrated the role of the microbiota in the development of NAFLD.

Bumble bee microbiota shows temporal succession and increase of lactic acid bacteria when exposed to outdoor environments.

The large earth bumble bee (Bombus terrestris) maintains a social core gut-microbiota, similar as known from the honey bee, which plays an important role for host health and resistance. Experiments under laboratory conditions with commercial hives are limited to vertically transmitted microbes and neglect influences of environmental factors or external acquisition of microbes. Various environmental and landscape-level factors may have an impact on the gut-microbiota of pollinating insects, with consequences for pollinator health and fitness in agroecosystems. Still, it is not fully clear whether access to different flower diversities will have a significant influence on the bumble bee microbiota. Here, we tested in a semi-field experiment if the bumble bee microbiota changes over time when exposed to different flower diversities within outdoor flight cages. We used commercial hives to distinguish between vertically and horizontally transmitted bacteria, respectively from the nest environment or the exposed outside environment. The sequential sampling of foraging workers over a period of 35 days indicated a temporal progression of the bumble bee microbiota when placed outside. The microbiota increased in diversity and changed in composition and variability over time. We observed a major increase in relative abundance of the families Lactobacillaceae, Bifidobacteriaceae and Weeksellaceae. In contrast, major core-taxa like Snodgrassella and Gilliamella declined in their relative abundance over time. The genus Lactobacillus showed a high diversity and strain specific turnover, so that only specific ASVs showed an increase over time, while others had a more erratic occurrence pattern. Exposure to different flower diversities had no significant influence on the progression of the bumble bee microbiota. The bumble bee microbiota showed a dynamic temporal succession with distinct compositional changes and diversification over time when placed outdoor. The exposure of bumble bees to environmental conditions, or environmental microbes, increases dissimilarity and changes the gut-community composition. This shows the importance of environmental influences on the temporal dynamic and progression of the bumble bee microbiota.

The toxicity of polystyrene micro- and nano-plastics on rare minnow (Gobiocypris rarus) varies with the particle size and concentration

How the particle size and concentration of microplastics impact their toxicity is largely unknown. Herein, the effects of polystyrene microplastics (1 μm, MPs) and nanoplastics (100 nm, NPs) exposed at 1 mg/L (L) and 10 mg/L (H), respectively, on the growth, histopathology, oxidative stress, gut microbiome, and metabolism of rare minnow (Gobiocypris rarus) were investigated by chemical analysis and multi-omics. MPs and NPs inhibited the growth, induced histopathological injury and aggravated oxidative stress markedly with contrasting significance of particle size and concentration. The composition of core gut microbiota changed dramatically especially for the MPs-H. Similarly, gut bacterial communities were reshaped by the MPs and NPs but only NPs-H decreased both richness and Shannon indexes significantly. Co-occurrence network analysis revealed that the potential keystone genera underwent great changes in exposed groups compared to the control. MPs-H increased the network complexity and the frequency of positive interactions which was opposite to other exposed groups. Moreover, the metabolomic profiles associated with amino acid, lipid, unsaturated fatty acid and hormone metabolism were disturbed significantly especially for MPs-H and NPs-H. In conclusion, the toxicity of MPs depends on both the particle size and concentration, and varies with the specific indicators as well.

Host-derived organic acids enable gut colonization of the honey bee symbiont Snodgrassella alvi.

Diverse bacteria can colonize the animal gut using dietary nutrients or by engaging in microbial crossfeeding interactions. Less is known about the role of host-derived nutrients in enabling gut bacterial colonization. Here we examined metabolic interactions within the evolutionary ancient symbiosis between the honey bee (Apis mellifera) and the core gut microbiota member Snodgrassella alvi. This betaproteobacterium is incapable of metabolizing saccharides, yet colonizes the honey bee gut in the presence of a sugar-only diet. Using comparative metabolomics, 13C-tracers and nanoscale secondary ion mass spectrometry (NanoSIMS), we show in vivo that S. alvi grows on host-derived organic acids, including citrate, glycerate and 3-hydroxy-3-methylglutarate, which are actively secreted by the host into the gut lumen. S. alvi also modulates tryptophan metabolism in the gut by converting kynurenine to anthranilate. These results suggest that S. alvi is adapted to a specific metabolic niche in the honey bee gut that depends on host-derived nutritional resources.

Exploring the gut microbiota of healthy captive Asian elephants from various locations in Yunnan, China.

The Asian elephant (Elephas maximus) is a giant herbivore classified as an endangered wildlife species by the International Union for Conservation of Threatened Species.This study aims to investigate and compare the core gut microbiota of captive Asian elephants from three different locations in Yunnan Province, China, to explore the impact of environmental and husbandry factors on microbial diversity. We collected fecal samples from 29 captive Asian elephants from three locations and performed full-length 16S rRNA gene sequencing. Microbial diversity was assessed using alpha diversity (Chao1 and Shannon indexes) and beta diversity (Bray-Curtis and Euclidean distance metrics). Principal coordinate analysis (PCoA) was used to visualize microbial variation among groups. Alpha diversity analysis showed that the microbial diversity in the Yexianggu group was higher than that in the other groups. Bray-Curtis and Euclidean metrics revealed significant differences among the microbial communities. Bacteroidetes and Firmicutes, which are key cellulose-degrading bacteria, were the dominant phyla in all groups. Synergistaceae was the most abundant family in the Menghai group, while Lachnospiraceae and Pirellulaceae were more abundant in the Yexianggu and Yuantongshan groups, respectively. Genus p-1008-a5-gut-group was more abundant in Yexianggu, and Prevotella was predominant in Menghai. These results indicate that habitat and husbandry practices significantly influence the gut microbiota of captive Asian elephants. The identification of bacterial species such as Lactobacillus fermentum, Clostridium neonatale, Enterococcus mundtii, Klebsiella huaxiensis, Corynebacterium nasicanis, and Streptococcus equinus highlights the potential role of specific microbes in maintaining host-microbial interactions. Promoting microbial diversity through improved captive conditions could enhance the health of these endangered animals.

Gut microbiota composition of Apis mellifera L. populations from Tunisia

Honey bee populations are major contributors to ecosystem stability, providing vital services such as pollination of crops and food security. Currently, honey bees are undergoing severe global decline which is likely due to the disruption of the gut microbiota underlying honey bee health status. The composition and diversity of honey bees’ gut microbiota are affected by several factors. In Tunisia, studies on honey bees’ gut microbiota remain largely unexplored. This study aimed to characterize the gut community composition of honey bee populations from Tunisia and to assess their diversity by sequencing the 16S rRNA gene amplicons. Our results revealed the presence of a core gut microbiota bound to the 4 phylotypes Snodgrassella, Gilliamella, Lactobacillus and Bifidobacterium which have different relative abundances across analyzed samples and uncovered the occurrence of pathogens in the sampled honey bee populations. Shannon and Simpson’s diversity indices showed consistent variation patterns in each analyzed sample that could be due to the local environment. This study is a first characterization of the honey bees’ gut microbiota from Tunisia and underscores the need to study the impact of environmental factors on microbiome diversity.

Effects of ingested essential oils and propolis extracts on honey bee (Hymenoptera: Apidae) health and gut microbiota.

Managed honey bee (Hymenoptera: Apidae: Apis mellifera Linnaeus) hives require frequent human inputs to maintain colony health and productivity. A variety of plant natural products (PNPs) are delivered via feeding to control diseases and reduce the use of synthetic chemical treatments. However, despite their prevalent use in beekeeping, there is limited information regarding the impact of ingested PNPs on bee health. Here, we tested the effects of different essential oils and propolis extracts on honey bee life span, nutrient assimilation, xenobiotic detoxification, and gut microbiota abundance. Brazilian propolis extract lengthened worker life span, while the other PNPs (Louisiana propolis extract, lemongrass oil, spearmint oil, and thyme oil) exerted variable and dose-dependent effects on life span. Vitellogenin (vg) gene expression was reduced by Brazilian propolis extract at high doses. Expression of CYP6AS1, a detoxification-related gene, was reduced by low doses of thyme oil. The abundances of 8 core gut microbiota taxa were largely unaffected by host consumption of PNPs. Our results suggest that in addition to propolis's structural and immunomodulatory roles in the colony, it may also exert beneficial health effects when ingested. Thyme oil, a commonly used hive treatment, was toxic at field-realistic dosages, and its use as a feed additive should be viewed with caution until its effects on bee health are more thoroughly investigated. We conclude that the tested propolis extracts, lemongrass oil, and spearmint oil are generally safe for bee consumption, with some apparent health-promoting effects.

Revealing the effects of fermented food waste on the growth and intestinal microorganisms of black soldier fly (Hermetia illucens) larvae

The escalating global food waste (FW) issues necessitate sustainable management strategies. Black soldier fly larvae (BSFL) offer a promising solution for FW management by converting organic matter into insect protein. However, the fermentation of FW during production, collection, and transportation induces changes in FW’s physicochemical properties and bacterial communities, requiring further exploration of its impact on BSFL growth and gut microbiota. The results showed that feeding FW fermented for different durations (0–10 d) slightly affected the BSFL yield. Feeding FW fermented for 8 d, characterized by a lower pH and higher biodiversity, resulted in a slight increase in larval biomass (222 mg/larvae). Nearly all groups harvested the peak larval biomass after 10 day’s bioconversion. The fermentation significantly altered the microbial community of FW, with an increase in the abundance of unclassified_f_Clostridiaceae and a decrease in Lactobacillus abundance. As bioconversion progressed, intricate and mutualistic microbial interactions likely occurred between the BSFL gut and FW substrate, restructuring each other’s microbial community. Specifically, the abundance of unclassified_f_Clostridiaceae increased in the BSFL gut, while its abundance in the initial larval gut was extremely low (<1 %). Despite the substrate microbial changes and interactions, a stable core gut microbiota was identified across all BSFL samples, primarily composed of nine genera dominated by Enterococcus and Klebsiella. This core gut microbiome may play a crucial role in facilitating the adaptation of BSFL to various environmental conditions and maintaining efficient FW bioconversion. These findings enhance our understanding of the role of BSFL gut microbiota in FW bioconversion.

The shared microbiome in mud crab (Scylla paramamosain) of Sanmen Bay, China: core gut microbiome.

The mud crab, Scylla paramamosain, holds great commercial significance as a marine crustacean widely cultivated in the Indo-Pacific region. Understanding the core gut microbiota of aquatic animals is crucial for their overall health and growth, yet the core gut microbiota of mud crab remains poorly characterized. In this study, we gathered gut samples from mud crabs across five locations within Sanmen Bay, China. Through the utilization of high-throughput sequencing, we delved into the composition of the gut microbial community and identified the core gut microbiome of mud crab. Our results demonstrate that the gut microbial diversity of mud crab did not exhibit significant variation among the five sampling sites, although there were some differences in community richness. At the phylum level, we identified 35 representative phyla, with Firmicutes, Proteobacteria, Bacteroidota, and Campilobacterota as the dominant phyla. Among the 815 representative genera, we discovered 19 core genera, which accounted for 65.45% of the total sequences. These core genera were distributed across 6 phyla, and among them, Photobacterium exhibited the highest average relative abundance. Photobacterium has probiotic activity and may play a crucial role in enhancing the immune response of the host and maintaining the diversity of the gut microbiota. Moreover, we observed a positive correlation between the relative abundance of core genera and the stability of the gut microbial community. Furthermore, our findings revealed distinct differences in gut microbial composition and specific taxa between the sexes of mud crab. These differences subsequently influenced the functionality of the gut microbial community. Overall, our investigation sheds light on the core gut microbiota of mud crab, emphasizing the importance of core gut microbial communities in maintaining the health and growth of these commercially significant marine crustaceans.

Host Habitat as a Dominant Role in Shaping the Gut Microbiota of Wild Crucian Carp (Carassius auratus)

Current knowledge on the fish gut microbiota has largely been obtained from experiments on laboratory-reared animals. Here, the crucian carp (Carassius auratus) with a mean weight of 159.9 ± 11.4 g (mean ± SD) were collected from their natural habitats (i.e., Wuhu lake and Poyang lake, China), and the gut microbiota were analysed by using the next-generation sequencing of 16S rRNA gene. We obtained more than 430,000 high-quality reads, which constituted more than 1200 operational taxonomy units (OTUs), revealing extremely diverse microbes in the fish gut. Proteobacteria, Fusobacteria, Bacteroidetes and Firmicutes were detected as the prominent phyla (each &gt; 1% of total abundance) within the gut microbiota, regardless of the host habitat or the gut segment (i.e., foregut vs. hindgut). Although the microbes in the hindgut were more diverse (OTU number, Shannon and Chao1; One-way Anova, p &gt; 0.05) than in the foregut, the host habitat had a significant role in shaping the community structures (MRPP, ANOSIM, PERMANOVA, p &lt; 0.01). Interestingly, we also detected a set of common OTUs, whereby genera Aeromonas and Cetobacterium might comprise the core gut microbiota of crucian carp.

Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika.

Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.

Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees

Nosema ceranae is an intracellular parasite invading the midgut of honeybees, which causes serious nosemosis implicated in honeybee colony losses worldwide. The core gut microbiota is involved in protecting against parasitism, and the genetically engineering of the native gut symbionts provides a novel and efficient way to fight pathogens. Here, using laboratory-generated bees mono-associated with gut members, we find that Snodgrassella alvi inhibit microsporidia proliferation, potentially via the stimulation of host oxidant-mediated immune response. Accordingly, N. ceranae employs the thioredoxin and glutathione systems to defend against oxidative stress and maintain a balanced redox equilibrium, which is essential for the infection process. We knock down the gene expression using nanoparticle-mediated RNA interference, which targets the γ-glutamyl-cysteine synthetase and thioredoxin reductase genes of microsporidia. It significantly reduces the spore load, confirming the importance of the antioxidant mechanism for the intracellular invasion of the N. ceranae parasite. Finally, we genetically modify the symbiotic S. alvi to deliver dsRNA corresponding to the genes involved in the redox system of the microsporidia. The engineered S. alvi induces RNA interference and represses parasite gene expression, thereby inhibits the parasitism significantly. Specifically, N. ceranae is most suppressed by the recombinant strain corresponding to the glutathione synthetase or by a mixture of bacteria expressing variable dsRNA. Our findings extend our previous understanding of the protection of gut symbionts against N. ceranae and provide a symbiont-mediated RNAi system for inhibiting microsporidia infection in honeybees.

Longevity-Associated Core Gut Microbiota Mining and Effect of Mediated Probiotic Combinations on Aging Mice: Case Study of a Long-Lived Population in Guangxi, China.

With an ageing population, healthy longevity is becoming an important scientific concern. The longevity phenomenon is closely related to the intestinal microflora and is highly complicated; it is challenging to identify and define the core gut microbiota associated with longevity. Therefore, in this study, 16S rRNA sequencing data were obtained from a total of 135 faecal samples collected as part of the latest sampling and pre-collection initiative in the Guangxi longevity area, and weighted gene co-expression network analysis (WGCNA) was used to find a mediumpurple3 network module significantly associated with the Guangxi longevity phenomenon. Five core genera, namely, Alistipes, Bacteroides, Blautia, Lachnospiraceae NK4A136 group, and Lactobacillus, were identified via network analysis and random forest (RF) in this module. Two potential probiotic strains, Lactobacillus fermentum and Bacteroides fragilis, were further isolated and screened from the above five core genera, and then combined and used as an intervention in naturally ageing mice. The results show a change in the key longevity gut microbiota in mice toward a healthy longevity state after the intervention. In addition, the results show that the probiotic combination effectively ameliorated anxiety and necrosis of hippocampal neuronal cells in senescent mice, improving their antioxidant capacity and reducing their inflammation levels. In conclusion, this longer-term study provides a new approach to the search for longevity hub microbiota. These results may also provide an important theoretical reference for the healthification of the intestinal microflora in the general population, and even the remodelling of the structure of the longevity-state intestinal microflora.

Co-diversification of an intestinal Mycoplasma and its salmonid host

Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems.

Gut microbiota play important roles in fish health and growth performance and the microbiome in fish has been shown to be a biomarker for stress. In this study, we surveyed the change of Chinook salmon (Oncorhynchus tshawytscha) gut and water microbiota in freshwater recirculating aquaculture systems (RAS) for 7 months and evaluated how gut microbial communities were influenced by fish health and growth performance. The gut microbial diversity significantly increased in parallel with the growth of the fish. The dominant gut microbiota shifted from a predominance of Firmicutes to Proteobacteria, while Proteobacteria constantly dominated the water microbiota. Photobacterium sp. was persistently the major gut microbial community member during the whole experiment and was identified as the core gut microbiota for freshwater farmed Chinook salmon. No significant variation in gut microbial diversity and composition was observed among fish with different growth performance. At the end of the trial, 36 out of 78 fish had fluid in their swim bladders. These fish had gut microbiomes containing elevated proportions of Enterococcus, Stenotrophomonas, Aeromonas, and Raoultella. Our study supports the growing body of knowledge about the beneficial microbiota associated with modern salmon aquaculture systems and provides additional information on possible links between dysbiosis and gut microbiota for Chinook salmon.

Enhanced protein degradation by black soldier fly larvae (Hermetia illucens L.) and its gut microbes.

Black soldier fly larvae (BSFL) can convert a variety of organic wastes into biomass, and its gut microbiota are involved in this process. However, the role of gut microbes in the nutrient metabolism of BSFL is unclear. In this study, germ-free BSFL (GF) and gnotobiotic BSFL (GB) were evaluated in a high-protein artificial diet model. We used 16S rDNA sequencing, ITS1 sequencing, and network analysis to study gut microbiota in BSFL that degrade proteins. The protein reduction rate of the GB BSFL group was significantly higher (increased by 73.44%) than that of the GF BSFL group. The activity of gut proteinases, such as trypsin and peptidase, in the GB group was significantly higher than the GF group. The abundances of different gut microbes, including Pseudomonas spp., Orbus spp. and Campylobacter spp., were strongly correlated with amino acid metabolic pathways. Dysgonomonas spp. were strongly correlated with protein digestion and absorption. Issatchenkia spp. had a strong correlation with pepsin activity. Campylobacter spp., Pediococcus spp. and Lactobacillus spp. were strongly correlated with trypsin activity. Lactobacillus spp. and Bacillus spp. were strongly correlated with peptidase activity. Gut microbes such as Issatchenkia spp. may promote the gut proteolytic enzyme activity of BSFL and improve the degradation rate of proteins. BSFL protein digestion and absorption involves gut microbiota that have a variety of functions. In BSFL the core gut microbiota help complete protein degradation. These results demonstrate that core gut microbes in BSFL are important in protein degradation.

Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure.

We examined the effects of a mixture of contaminants found in agricultural watersheds on the gut microbiota and physiology of both the freshwater mussel Lampsilis cardium, and L. cardium host fish Micropterus salmoides. Lampsilis cardium and M. salmoides were exposed to three concentrations of agricultural contaminants for 60 days (observing behaviour daily) before being sampled for gut microbiota analyses. DNA was extracted from the gut samples, amplified via PCR, and sequenced using the Illumina Mi-Seq platform. Only L. cardium guts had differing microbiota across treatments, with an increase in potentially pathogenic Aeromonas. We also provide novel evidence of a core microbiota within L. cardium and M. salmoides. In terms of physiology, female L. cardium exhibited a decrease in movement and marsupial gill display in contaminant exposures. Exposure to contaminants from agricultural watersheds may affect population recruitment within freshwater mussel communities over time. Specifically, increased pathogenic micro-organisms and altered behaviour can reduce the likelihood of glochidia dispersal. This study supports emerging research that contaminants found in agricultural watersheds may be a factor in freshwater mussel population declines. It also provides novel evidence that unionids have a core gut microbiota.

Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition.

The genus Cetobacterium has been considered a dominant group of gut bacteria in many freshwater fish, and members of this genus contribute to anaerobic metabolism. Because of its significant place in the gut of freshwater fish, many studies on Cetobacterium were performed. Those studies mostly focused on the temporal and spatial changes of its abundance in fish intestine, which were affected byfood or other environmentalconditions. However, only a few studies isolated strains from genus Cetobacterium and reported their characteristics. In the present study, we performed 16S rRNA sequencing of the intestinal mucosa of Nile tilapia (Oreochromis niloticus) and found that Cetobacterium sp. existed widely in the foregut, midgut and hindgut mucosa, and a strain of Cetobacterium was successfully isolated from the gut of tilapia. We sequenced its whole genome and predicted it to be a novel candidate species of Cetobacterium sp. and named it NK01. The size of its genome was 3,095,946bp, with a guanine + cytosine content of 28.8%. Among the identified genes, 2855 were predicted to be coding DNA sequences, 84 were tRNA and 34 were rRNA. We found that NK01 produced amino acids, including leucine, isoleucine, valine, glycine, alanine, phenylalanine and proline. Strain NK01 could use starch, sucrose, maltose, glucose, and mannose and synthesize and utilize glycogen. INV, GPI, malQ, malZ, sacA, scrK, glgC, glgA and glk, which were related to carbohydrate metabolism, were detected. yiaY and adhE, which oxidize ethanol to acetaldehyde and participate in a variety of metabolic pathways, were also present in the genome. No coding genes directly involved in acetate or butyrate production were detected. NK01 could also catabolize a variety of vitamins, and all genes involved in folate synthesis were detected, including folP, folC, folA and eutT, which converted vitamin B12s into vitamin B12 coenzyme. Here, we investigated the draft genome and in vitro function of Cetobacterium isolated from the intestinal tract of Nile tilapia. The results provided a preliminary understanding of the core microbiota of fish gut.