A Comparative Metagenomics Study on Gastrointestinal Microbiota in Amphibious Mudskippers and Other Vertebrate Animals

Unexpected Microbial and Genetic Diversity in the Gut of Chinese Giant Salamander

The gut microbiome is crucial for animal health, yet the diversity of the critically endangered Chinese giant salamander's gut microbiota remains largely uncharacterized. In this study, we first conducted a comprehensive landscape survey of the gut microbiome of the Chinese giant salamander using 16S rRNA sequencing across a wide geographic range, identifying a distinct microbial cluster within its habitat. Subsequently, using shotgun metagenomes, we recovered 1518 metagenome-assembled genomes. Notably, 85% of the newly identified genomes could not be assigned to any known bacterial species, indicating a significant presence of novel taxa in Chinese giant salamander intestines. We observed substantial species-level variations in the gut microbiome across different age groups, with some novel species uniquely enriched in specific age populations. From the gut symbionts, we established a gene catalog comprising 3 278 107 non-redundant protein-coding genes, of which 7733 were annotated into recognized KEGG orthology groups. Additionally, we found that the gut microbiota of the Chinese giant salamander exhibits enhanced functional capacities explicitly in lipid metabolism and assimilatory sulfate reduction. Significant variations in the abundance of related enzyme-encoding genes across age groups suggest the unique roles of microbial metabolism in salamander health. By identifying microbial genomes and constructing an integrated gene catalog from metagenomic data, we significantly expand the resources available for research on the gut microbiome of the Chinese giant salamander, paving the way for further investigations into its ecological and health-related implications.

Differences and correlation analysis of feeding habits and intestinal microbiome in Schizopygopsis microcephalus and Ptychobarbus kaznakovi in the upper reaches of Yangtze River

Background

The intestinal microbiota has co-evolved with the host to establish a stable and adaptive microbial community that is essential for maintaining host health and facilitating food digestion. Food selection is a critical factor influencing variations in gut microbial composition, shaping gut microbiome communities, and determining the ecological niches of fish.

Methods

In this study, high-throughput amplicon sequencing of 16S rRNA and 18S rRNA was utilized to compare the dietary and gut microbial differences between Schizopygopsis microcephalus and Ptychobarbus kaznakovi, both collected from the same sites in the Tuotuo River and Tongtian River, which are tributaries of the Yangtze River. We compared the microbial community structure, diet composition, and diversity between the two fish species using various analytical methods, including LefSe, α-diversity and β-diversity analyses. Additionally, we constructed co-occurrence networks to determine their correlations.

Results and discussion

The alpha diversity results indicated that S. microcephalus exhibited higher intestinal microbiota and feeding diversity compared to P. kaznakovi. Furthermore, the beta diversity results revealed significant differences in both intestinal microbiota and eukaryotic communities between the two species. The dominant bacterial phyla in both S. microcephalus and P. kaznakovi included Proteobacteria, Firmicutes, Actinobacteriota, Chloroflexi, and Verrucomicrobiota; however, Firmicutes was significantly more abundant in P. kaznakovi (P = 0.006), while Actinobacteriota was significantly higher (P = 0.019) in S. microcephalus at the phylum level. The primary food sources for S. microcephalus and P. kaznakovi were identified as Streptophyta (54.41%, 77.50%) and Cercozoa (8.67%, 1.94%), with Bacillariophyta (25.65%) was also the main food of constituting a major component of the diet for S. microcephalus. These differences suggested that S. microcephalus and P. kaznakovi occupy distinct dietary niches. To further explore the relationship between gut microbiota and feeding habits, we identified significant correlations between various food components and the gut microbial community through co-occurrence networks. This study enhances our understanding of the co-evolution and co-adaptation between host gut microbiota and feeding behaviors in sympatric fish species.

The Marine Fish Gut Microbiome as a Source of Novel Bacteriocins

The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area.

Metagenomics Analysis Reveals the Composition and Functional Differences of Fecal Microbiota in Wild, Farm, and Released Chinese Three-Keeled Pond Turtles (Mauremys reevesii)

The intestine of living organisms harbors different microbiota associated with the biological functioning and health of the host and influences the process of ecological adaptation. Here, we studied the intestinal microbiota's composition and functional differences using 16S rRNA and metagenomic analysis in the wild, farm, and released Chinese three-keeled pond turtle (Mauremys reevesii). At the phylum level, Bacteroidota dominated, followed by Firmicutes, Fusobacteriota, and Actinobacteriota in the wild group, but Chloroflexi was more abundant in the farm and released groups. Moreover, Chryseobacterium, Acinetobacter, Comamonas, Sphingobacterium, and Rhodobacter were abundant in the released and farm cohorts, respectively. Cetobacterium, Paraclostridium, Lysobacter, and Leucobacter showed an abundance in the wild group. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed that the relative abundance of most pathways was significantly higher in the wild turtles (carbohydrate metabolism, lipid metabolism, metabolism of cofactors, and vitamins). The comprehensive antibiotic resistance database (CARD) showed that the antibiotic resistance gene (ARG) subtype macB was the most abundant in the farm turtle group, while tetA was higher in the wild turtles, and srpYmcr was higher in the released group. Our findings shed light on the association between the intestinal microbiota of M. reevesii and its habitats and could be useful for tracking habitats to protect and conserve this endangered species.

Virulence, antibiotic resistance phenotypes and molecular characterisation of Vibrio furnissii isolates from patients with diarrhoea

BACKGROUND

Vibrio furnissii is an emerging human pathogen closely related to V. fluvialis that causes acute gastroenteritis. V. furnissii infection has been reported to be rarer than V. fluvialis, but a multi-drug resistance plasmid has recently been discovered in V. furnissii.

METHODS

During daily monitoring at a general hospital in Beijing, China, seven V. furnissii strains were collected from patients aged over 14 years who presented with acute diarrhoea between April and October 2018. Genome analysis and comparison were performed for virulence and antimicrobial resistance genes, plasmids and transposon islands, together with phylogenetic analysis. Antimicrobial resistance to 19 antibiotics was investigated using the microbroth dilution method. Virulence phenotypes were investigated based on type VI secretion system (T6SS) expression and using a bacterial killing assay and a haemolysin assay.

RESULTS

Phylogenetic analysis based on single-nucleotide polymorphisms revealed a closer relationship between V. furnissii and V. fluvialis than between other Vibrio spp. The seven V. furnissii isolates were in different monophyletic clades in the phylogenetic tree, suggesting that the seven cases of gastroenteritis were independent. High resistance to cefazolin, tetracycline and streptomycin was found in the V. furnissii isolates at respective rates of 100.0%, 57.1% and 42.9%, and intermediate resistance to ampicillin/sulbactam and imipenem was observed at respective rates of 85.7% and 85.7%. Of the tested strains, VFBJ02 was resistant to both imipenem and meropenem, while VFBJ01, VFBJ02, VFBJ05 and VFBJ07 were multi-drug resistant. Transposon islands containing antibiotic resistance genes were found on the multi-drug resistance plasmid in VFBJ05. Such transposon islands also occurred in VFBJ07 but were located on the chromosome. The virulence-related genes T6SS, vfh, hupO, vfp and ilpA were widespread in V. furnissii. The results of the virulence phenotype assays demonstrated that our isolated V. furnissii strains encoded an activated T6SS and grew in large colonies with strong beta-haemolysis on blood agar.

CONCLUSION

This study showed that diarrhoea associated with V. furnissii occurred sporadically and was more common than expected in the summer in Beijing, China. The antibiotic resistance of V. furnissii has unique characteristics compared with that of V. fluvialis. Fluoroquinolones and third-generation cephalosporins, such as ceftazidime and doxycycline, were effective at treating V. furnissii infection. Continua laboratory-based surveillance is needed for the prevention and control of V. furnissii infection, especially the dissemination of the antibiotic resistance genes in this pathogen.

Effects of high NaHCO3 alkalinity on growth, tissue structure, digestive enzyme activity, and gut microflora of grass carp juvenile

With the gradual decrease in freshwater resources, the available space for freshwater aquaculture is diminishing. As a result, saline-alkaline water aquaculture has emerged as a crucial method to fulfill the increasing demand. This study investigates the impact of alkaline water on the growth performance, tissues (gill, liver, and kidney), digestive enzyme activity, and intestinal microbiology in grass carp (Ctenopharyngodon idella). The aquarium conditions were set with sodium bicarbonate (18 mmol/L (LAW), 32 mmol/L (HAW)) to simulate the alkaline water environment. A freshwater group was the control (FW). The experimental fish were cultured for 60 days. The findings revealed that NaHCO3 alkaline stress significantly reduced growth performance, caused alterations in the structural morphology of gill lamellae, liver, and kidney tissues, and led to decreased activity of intestinal trypsin and lipase amylase (P < 0.05). Analysis of 16S rRNA sequences demonstrated that alkalinity influenced the abundance of dominant bacterial phyla and genera. Proteobacteria showed a significant decrease under alkaline conditions, while Firmicutes exhibited a significant increase (P < 0.05). Furthermore, alkalinity conditions significantly reduced the abundance of bacteria involved in protein, amino acid, and carbohydrate metabolism, cell transport, cell decomposition, and environmental information processing. Conversely, the abundance of bacteria associated with lipid metabolism, energy metabolism, organic systems, and disease functional flora increased significantly under alkalinity conditions (P < 0.05). In conclusion, this comprehensive study indicates that alkalinity stress adversely affected the growth performance of juvenile grass carp, likely due to tissue damage, reduced activity of intestinal digestive enzymes, and alterations in intestinal microorganisms.

Protective effects of 5-aminolevulinic acid against toxicity induced by alpha-cypermethrin to the liver-gut-microbiota axis in zebrafish

To explore whether and how 5-aminolevulinic acid (ALA) can relieve the toxicity to the liver-gut-microbiota axis caused by alpha-cypermethrin (α-CP), adult zebrafish were exposed to α-CP (1.0 µg L-1) with or without 5.0 mg L-1 ALA supplementation. In the present work, the calculated LC50 of α-CP+ALA was 1.15 μg L-1, increasing about 1.16-fold compared with that of α-CP group (0.99 μg L-1), which indicated that ALA can alleviate the toxicity of α-CP. ALA also alleviated the histopathological lesions in the liver and gut induced by α-CP. Transcriptome sequencing of the liver showed that ALA rescues the differential expression of genes involved in the oxidation-reduction, heme metabolism, and complement activation pathways associated with dysfunctions induced by α-CP, and these findings were verified by RT-qPCR analysis and detection of the activities of enzymes in the liver-gut axis. The gut microbiota 16S rRNA sequencing results showed that α-CP alone induced gut microbial dysbiosis, which was efficiently antagonized by ALA due to decreasing the relative abundances of Cetobacterium and 3 major pathogens, and increasing the relative abundances of beneficial genera. Taken together, the results indicate that ALA might be a promising candidate for attenuating the adverse effects caused by pesticide-induced environmental pollution.

Effects of underwater and semi-aquatic environments on gut tissue and microbiota of the mudskipper Boleophthalmus pectinirostris

In both underwater and semi-aquatic environments, the gut microbiota is of particular physiological importance for amphibious animals, given that the gut tract is among those organs in direct communication with the external environment. In this study, we examined the effects of these contrasting environments on the dominant bacteria in the guts of the amphibious mudskipper Boleophthalmus pectinirostris. Compared with the guts of normal mudskippers, in which the dominant bacteria were identified as Vibrio and Faecalibacterium, we found that Acinetobacter, Shigella, and Bacillus predominated in their guts after exposure to the semi-aquatic environment, whereas Escherichia, Bacteroides, and Bacillus were more prevalent in the guts in the underwater environment. The total number of cultured gut bacteria decreased significantly in the semi-aquatic environment. In semi-aquatic mudskippers, we also detected reductions and increases in the length and width of gut villi, respectively, whereas the width of gut villi declined and the number of goblet cells increased significantly in mudskippers maintained underwater. The mRNA expression of multiple gut transporters for glucose, long-chain fatty acids, and amino acids was found to increase markedly in both underwater and semi-aquatic environments, with the expression of most transporters being significantly higher in those mudskippers exposed to an underwater environment. Furthermore, we detected significant increases in the mRNA expression of pro-inflammatory cytokine transcripts in the guts of both underwater and semi-aquatic mudskippers on days 2, 4, and 6 of exposure, whereas the expression of IL-10 and TGFβ mRNA was more pronounced on days 4 and 8, respectively. Comparatively, we found that expression levels of cytokines in the guts of underwater mudskipper were substantially higher than those in the guts of semi-aquatic mudskippers. Collectively, our findings revealed notable differences in the gut microbiota and energy metabolism requirements of mudskippers exposed to underwater and semi-aquatic conditions, thereby providing a theoretical basis explaining the maintenance of a homeostatic state in mudskippers that constantly transition between these contrasting amphibious habitats.

The role of intestinal microbiota of the marine fish (Acanthopagrus latus) in mercury biotransformation

Both inorganic (IHg) and organic (MeHg) forms of Hg can be converted into each other by methylation or demethylation, leading to changes of Hg speciation and distribution in fish. However, Hg biotransformation in fish is not thoroughly understood and the key factors in this process are unclear. The present study investigated the in vivo Hg transformation in a marine fish (Acanthopagrus latus) and explored the roles of intestinal microbiota in Hg biotransformation. We first demonstrated that Hg methylation or demethylation occurred in the fish gut under dietary IHg or MeHg exposure, respectively. The demethylation was observed to be faster than methylation, suggesting that demethylation could significantly influence the Hg speciation in fish. This study also strongly suggested that intestinal microbiota played a predominant role in Hg biotransformation and thus significantly affected the overall Hg accumulation and distribution in fish body. The richness of Hg methylators or demethylators was elevated under IHg or MeHg treatment, respectively. Furthermore, the intestinal microbiota composition was also altered by Hg exposure. This study highlights the importance of intestinal microbiota in Hg biotransformation in fish body, and suggests that modulating the gut microbiome could be a possible solution to minimize Hg contamination in fish.

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.