Comparative analysis of the composition and function of fecal-gut bacteria in captive juvenile Crocodylus siamensis between healthy and anorexic individuals

Exploring Dietary Composition in an Invasive Apple Snail From Different Habitats Combining With Intestinal Microbiota and Metabolomics

Pomacea canaliculata is recognized as a globally invasive aquatic species. Analyses of intestinal microbiota, dietary composition, and metabolism of invasive species can enhance our understanding of their feeding strategies and physiological adaptation strategies to the environment. Intestinal content samples were collected from P. canaliculata inhabiting three distinct environments including a pond, a river, and a ditch. These samples were subjected to 16S rRNA gene sequencing analysis and multiple metabarcoding analyses, including eukaryotic 18S rRNA, mitochondrial cytochrome c oxidase I (COI), and chloroplast rbcL genes. In addition, metabolomics analysis was conducted on the intestinal content samples to investigate metabolic change. The highest dietary diversity in P. canaliculata was observed in the ditch, and females exhibited a higher dietary diversity than males in the pond. The 18S rRNA gene has a high potential for identifying the dietary components of omnivorous species. The intestinal microbiota of P. canaliculata from different habitats displayed significant variations, attributed to differences in food resources and other environmental factors. Bacteria in the aquatic environment had minimal impact on the intestinal microbiota of P. canaliculata. Overall, P. canaliculata exhibited adaptive changes in physiological characteristics across different habitats, including alterations in diet, which, in turn, influence microbiota and metabolic pathways such as amino acid biosynthesis in the intestine. The present study investigated the physiological mechanisms that enable P. canaliculata to adapt to diverse habitats, considering various factors including diet, which is important for comprehending its invasive potential and the subsequent threats it poses to aquatic ecosystems.

Effects of glyphosate-based herbicide on gut microbes and hepatopancreatic metabolism in Pomacea canaliculata

Roundup®, a prominent glyphosate-based herbicide (GBH), holds a significant position in the global market. However, studies of its effects on aquatic invertebrates, including molluscs are limited. Pomacea canaliculata, a large freshwater snail naturally thrives in agricultural environments where GBH is extensively employed. Our investigation involved assessing the impact of two concentrations of GBH (at concentrations of 19.98 mg/L and 59.94 mg/L, corresponding to 6 mg/L and 18 mg/L glyphosate) during a 96 h exposure experiment on the intestinal bacterial composition and metabolites of P. canaliculata. Analysis of the 16 S rRNA gene demonstrated a notable reduction in the alpha diversity of intestinal bacteria due to GBH exposure. Higher GBH concentration caused a significant shift in the relative abundance of dominant bacteria, such as Bacteroides and Paludibacter. We employed widely-targeted metabolomics analysis to analyze alterations in the hepatopancreatic metabolic profile as a consequence of GBH exposure. The shifts in metabolites primarily affected lipid, amino acid, and glucose metabolism, resulting in compromised immune and adaptive capacities in P. canaliculata. These results suggested that exposure to varying GBH concentrations perpetuates adverse effects on intestinal and hepatopancreatic health of P. canaliculata. This study provides an understanding of the negative effects of GBH on P. canaliculata and may sheds light on its potential implications for other molluscs.

Responses of gut microbiota in crocodile lizards (Shinisaurus crocodilurus) to changes in temperature

The gut microbiota plays an essential role in maintaining the health and fitness of the host organism. As a critical environmental variable, temperature exerts significant effects on animal survival and reproduction. Elevated temperatures can influence the composition and function of the animal gut microbiota, which may have potentially detrimental effects on the host. The crocodile lizard (Shinisaurus crocodilurus) is an ancient and currently endangered reptile species due to human hunting and habitat destruction. Given the predicted shifts in global temperatures in the next century, it is important to understand how warming affects the gut microbiota of these vulnerable lizards, which remains unclear. To determine how the microbial communities change in crocodile lizards in response to warming, we analyzed the gut microbiota under five temperature conditions (22°C, 24°C, 26°C, 28°C, and 30°C) using 16S rRNA high-throughput sequencing. Results showed that the dominant phyla, Proteobacteria and Bacteroidetes, in gut microbiota were not significantly affected by temperature variations, but increasing temperature altered the structure and increased the community richness of the gut microbiota. In addition, warming changed the abundance of Pseudomonas aeruginosa and Actinobacteria, which may have negative effects on the physiological health of the crocodile lizards. Functional prediction analysis demonstrated that the functional pathways enriched in crocodile lizards were mainly related to metabolism, with no significant differences observed in these pathways at KEGG pathway level 1 after warming. These results provide valuable insights into the ecological adaptations and regulatory mechanisms employed by crocodile lizards in response to warming, which may be of benefit for their conservation.

Xenobiotic estradiol-17ß alters gut microbiota of hatchling American alligators (Alligator mississippiensis)

Environmental oestrogens pose serious concerns for ecosystems through their effects on organismal survival and physiology. The gut microbiome is highly vulnerable to environmental influence, yet the effects of oestrogens on gut homeostasis are unknown because they are poorly studied in wildlife populations. To determine the influence of environmental oestrogens (i.e., xenoestrogens) on the diversity and abundance of gut microbiota, we randomly assigned 23 hatchling American alligators (Alligator mississippiensis) to three ecologically relevant treatments (control, low, and high oestrogen concentrations) for 10 weeks. We predicted that xenoestrogen exposure would decrease microbial diversity and abundance within the digestive tract and that this effect would be dose-dependent. Microbial samples were collected following diet treatments and microbial diversity was determined using 16S rRNA gene-sequencing. Individuals in oestrogen-treatment groups had decreased microbial diversity, but a greater relative abundance of operational taxonomic units than those in the control group. In addition, this effect was dose-dependent; as individuals were exposed to more oestrogen, their microbiome became less diverse, less rich and less even. Findings from this study suggest that oestrogen contamination can influence wildlife populations at the internal microbial-level, which may lead to future deleterious health effects.

Sexual Dimorphism of the Gut Microbiota in the Chinese Alligator and Its Convergence in the Wild Environment

The gut microbiota forms a complex microecosystem in vertebrates and is affected by various factors. As a key intrinsic factor, sex has a persistent impact on the formation and development of gut microbiota. Few studies have analyzed sexual dimorphism of gut microbiota, particularly in wild animals. We used 16S rRNA gene sequencing to analyze the gut microbiota of juvenile and adult Chinese alligators, and untargeted metabolomics to study serum metabolomes of adult alligators. We observed significant sexual differences in the community diversity in juvenile, but not adult, alligators. In terms of taxonomic composition, the phylum Fusobacteriota and genus Cetobacterium were highly abundant in adult alligators, similar to those present in carnivorous fishes, whereas the gut microbiota composition in juvenile alligators resembled that in terrestrial reptiles, indicating that adults are affected by their wild aquatic environment and lack sex dimorphism in gut microbiota. The correlation analysis revealed that the gut microbiota of adults was also affected by cyanobacteria in the external environment, and this effect was sex-biased and mediated by sex hormones. Overall, this study reveals sexual differences in the gut microbiota of crocodilians and their convergence in the external environment, while also providing insights into host-microbiota interactions in wildlife.

Seasonal variation in structure and function of gut microbiota in Pomacea canaliculata

Gut microbiota is associated with host health and its environmental adaption, influenced by seasonal variation. Pomacea canaliculata is one of the world's 100 worst invasive alien species. Here, we used high-throughput sequencing of the 16S rRNA gene to analyze the seasonal variation of gut microbiota of P. canaliculata. The results suggested that the predominant gut microbial phyla of P. canaliculata included Firmicutes and Proteobacteria, which helped digest plant food and accumulate energy. The gut microbiota of P. canaliculata in summer group showed the highest diversity, whereas the winter group possessed the lowest, probably due to the shortage of food resources of P. canaliculata in winter. Principal coordinate analysis analysis based on unweighted unifrac and weighted unifrac indicated that the composition of gut microbiota of P. canaliculata significantly varied across seasons. Bacteroidetes tended to be enriched in summer by linear discriminant analysis effect size analysis. Actinobacteria and Cyanobacteria were extremely abundant in autumn, while Fusobacteria and Cetobacterium enriched in winter. In conclusion, the structure of the gut microbiota of P. canaliculata was significantly different among seasons, which was beneficial to the environment adaptation and the digestion and metabolism of food during different periods.

Comparison of Gut Microbiota Diversity Between Captive and Wild Tokay Gecko (Gekko gecko)

Captive animals and wild animals may exhibit different characteristics due to the heterogeneity of their living environments. The gut microbiota play an important role in the digestion and absorption, energy metabolism, immune regulation, and physiological health of the host. However, information about the gut microbiota of captive and wild Gekko gecko is currently limited. To determine the difference in gut microbiota community composition, diversity, and structure between captive and wild geckos, we used the Illumina miseq platform to conduct high-throughput sequencing and bioinformatics analysis of the v3–v4 hypervariable region of 16S rRNA in 54 gecko samples. Our results showed that Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria were the dominant gut microbiota phyla of the gecko. The dominant genera comprised mainly Pseudomonas, Burkholderia-caballeronia-paraburkholderia, Ralstonia, Romboutsia, and Bacteroides. Captive geckos had significantly higher alpha diversity and potential pathogenic bacteria than wild populations. Moreover, significant differences in beta diversity of gut microbiota were observed between two populations. Functional prediction analysis showed that the relative abundance of functional pathways of wild geckos was more higher in metabolism, genetic information processing and organismal system function than those in captive geckos. Total length significantly affected gut microbial community (R² = 0.4527, p = 0.001) and explained 10.45% of the total variation for gut microbial community variance between two groups. These results may be related to differences in diet and living environment between two populations, suggesting that the management of captive populations should mimic wild environments to the greatest extent possible to reduce the impact on their gut microbiota.

Crocodylus porosus Gut Bacteria: A Possible Source of Novel Metabolites

Crocodiles are remarkable animals that have the ability to endure extremely harsh conditions and can survive up to a 100 years while being exposed to noxious agents that are detrimental to Homo sapiens. Besides their immunity, we postulate that the microbial gut flora of crocodiles may produce substances with protective effects. In this study, we isolated and characterized selected bacteria colonizing the gastrointestinal tract of Crocodylusporosus and demonstrated their inhibitory effects against three different cancerous cell lineages. Using liquid chromatography-mass spectrometry, several molecules were identified. For the first time, we report partial analyses of crocodile's gut bacterial molecules.

Crocodile Gut Microbiome Is a Potential Source of Novel Bioactive Molecules

Here, it is proposed that the crocodile gut microbiome is a valuable biomaterials resource to counter threats posed by environmental and infectious hazards to the existence of Homo sapiens.

Assessment of quality characteristics and bacterial community of modified atmosphere packaged chilled pork loins using 16S rRNA amplicon sequencing analysis

Modified atmosphere packaging (MAP) is widely applied in packaging meat and meat products. While most studies had employed culture-dependent microbiological analyses or polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the recent application of high-throughput sequencing (HTS) has been effective and reliable in detecting the microbial consortium associated with food spoilage. Since MAP application is limited in China, applying HTS in assessing the microbial consortium of meat and meat products in the country becomes imperative. In this study, quality indexes and bacterial enumeration often used as spoilage indicators were employed to assess MAP fresh pork under chilled (4 °C) storage for 21 d. The results indicated that 70%O₂/30%CO₂ (Group A) retained more redness (a*) content, while 70%N₂/30%CO₂ (Group B) markedly reduced spoilage indicators compared to the control group. Notably, high-throughput sequencing indicated that Group B and 20%O₂/60%N₂/20%CO₂ (Group C) inhibited the growth of abundant spoilers, Pseudomonas spp. and Brochothrix spp. Thus, MAP (Group B and C) has promising potential in inhibiting predominant meat spoilers during chilled storage. This study provides valuable information to food industries on the potential application of MAP to control meat spoilage in Chinese markets.

The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota

BACKGROUND

The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle (Chinemys reevesii) and the invasive red-eared slider turtle (Trachemys scripta elegans) are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected.

METHODS

We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform.

RESULTS

The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in C. reevesii, whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in T. s. elegans. In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in T. s. elegans than in C. reevesii, as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in T. s. elegans than in C. reevesii, presumably suggesting an enhanced potential to colonize new habitats in the former species.

Microbiota of Four Tissue Types in American Alligators (Alligator mississippiensis) Following Extended Dietary Selenomethionine Exposure

Selenium represents an essential trace nutrient that is necessary for biological functions. Deficiencies can induce disease, but excess can induce toxicity. Selenium deficiency is a major concern in underdeveloped countries, while also posing as a toxic pollutant in waterways surrounding landfills, agricultural areas, and fossil fuel production sites. We examined the microbiome of selenomethionine (SeMet) fed American alligators (Alligator mississippiensis) at the beginning and end of a 7-week exposure experiment. Alligators were randomly divided into three groups: control and 1000 or 2000 ppm SeMet. DNA from before exposure (oral and cloaca swabs) and post-exposure (oral, cloaca, small & large intestines) sampling were extracted and amplified for bacterial 16 s rRNA. While treatment did not seem to have much effect, we observed a predominance of Fusobacteriaceae and Porpyromonodaceae across all tissue types. Cetobacterium and Clostridium are the most abundant genera as potential indicators of the aquatic and carrion feeding lifestyle of alligators.

The gut bacterial microbiota of sea turtles differs between geographically distinct populations

The microbiota of metazoans can be influenced by a variety of factors including diet, environment and genetics. In this study we sampled multiple populations from 2 host species that do not overlap in distribution, in order to test whether their bacterial microbiotas are species-specific or more variable. Intestinal swabs were collected from loggerhead turtles originating from Florida, USA, and Queensland, Australia, as well as from flatback turtles from Crab Island, Queensland, and Port Hedland, Western Australia. We then manually extracted bacterial DNA and used 16S rRNA sequencing to explore bacterial microbial community composition and structure. Our investigation showed that the bacterial microbiota of sea turtles is heavily influenced by geography, with loggerhead turtles originating from the USA and Australia harbouring significantly different bacterial microbial populations in terms of composition. Similarly, we also found that flatback turtles from Crab Island had significantly less diverse microbiotas, with a predominance of the bacterial phylum Firmicutes, in comparison to their genetically similar counterparts from Port Hedland. Factors that may explain these observed differences between populations include host genetics, differences in foraging habitat quality and differences in migratory distance (and thus durations of inappetence) between foraging and breeding grounds. The mechanisms by which these factors may influence bacterial microbial composition of sea turtle gastrointestinal tracts warrants further investigation. The results of this study highlight the importance of interpreting microbiota data of wild animals in the context of geography.

Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history

Background

The microbiota plays a critical role in host homeostasis and has been shown to be a major driving force in host evolution. However, our understanding of these important relationships is hampered by a lack of data for many species, and by significant gaps in sampling of the evolutionary tree. In this investigation we improve our understanding of the host-microbiome relationship by obtaining samples from all seven extant species of sea turtle, and correlate microbial compositions with host evolutionary history.

Results

Our analysis shows that the predominate phyla in the microbiota of nesting sea turtles was Proteobacteria. We also demonstrate a strong relationship between the bacterial phyla SR1 and sea turtle phylogeny, and that sea turtle microbiotas have changed very slowly over time in accordance with their similarly slow phenotypic changes.

Conclusions

This is one of the most comprehensive microbiota studies to have been performed in a single clade of animals and further improves our knowledge of how microbial populations have influenced vertebrate evolution.

Comparative analysis of the composition and function of fecal-gut bacteria in captive juvenile Crocodylus siamensis between healthy and anorexic individuals

The Siamese crocodile (Crocodylus siamensis) is a freshwater, endangered crocodile with high economic value in the farming industry. Gut microflora plays an essential role in host physiological activity, and it contributes significantly to both the health and diseased states of animals. However, thus far, no study has focused on the correlation between diseases and intestinal bacterial communities in crocodilians. Here, we first compared the composition and function of gut microbial communities in captive juvenile C. siamensis suffering from anorexia and healthy crocodile controls using deep amplicon sequencing. The gut microbial diversity of anorexic crocodiles was much lower than the healthy individuals. Obvious changes in gut microbial composition were observed between sick and healthy crocodiles, except for Cetobacterium somerae of phylum Fusobacteria. In particular, the abundance of Bacteroides luti, Clostridium disporicum, Plesiomonas shigelloides, and Odoribacter sp. in the gut flora of healthy crocodiles was distinctly higher than the diseased group. Conversely, the species Edwardsiella tarda was overrepresented in the gut of anorexic crocodiles compared to the healthy group. Furthermore, in anorexic crocodiles, the predicted microbial functions that were related to amino acid metabolism, biosynthesis of other secondary metabolites, nucleotide metabolism, replication and repair, and translation were significantly reduced, while signal transduction was significantly enriched. These findings of the present study provide a reference to enrich the field of gut microorganism studies in crocodilians and suggest that alterations in the composition and function of gut bacteria in C. siamensis juveniles may be associated with anorexia in crocodiles.