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In the context of ongoing global warming, fish, as aquatic ectotherms, are highly vulnerable to increased water temperature caused by climate change and extreme heatwaves because of their inability to maintain their body temperature. After prolonged coevolution, the intestinal microbiota has become an integral part of fish and plays a pivotal role in immunity and metabolism. To date, however, little is known about the effects of increased water temperature on the intestinal microbiota of fish, particularly the intestinal mucosa-associated microbiota. Here, we investigated the variation patterns of the intestinal microbiota and immune status in Nile tilapia ( Oreochromis niloticus ; 125.02 ± 4.55 g) under increased water temperature. The results showed that the microbial diversity, structure, dominant microbes, and predicted function of fish intestinal microbiota were resilient to low-level warming (increasing by 2 °C) but not to high-level warming (increasing by 8 °C) and that fish immune parameters (serum lysozyme content and bactericidal activity) recovered simultaneously. Notably, along with compromised immune function, short-term warming (7 days) drove a significant increase in the microbial richness and diversity of fish intestinal mucosae, in which the overgrowth of opportunistic pathogens such as Romboutsia ilealis , Escherichia – Shigella , Fusobacterium , Streptococcus , Acinetobacter , and Enterobacter inhibited the colonization of potential probiotics such as Cetobacterium , ultimately resulting in a significant reduction in metabolic pathways and a significant increase in the potentially pathogenic phenotype. After long-term warming (37 days), the above alterations disappeared in low-level warming but remained in high-level warming. Critically, long-term warming disrupted the network complexity and stability of the intestinal mucosa- and digesta-associated microbiota to different extents. Collectively, this study revealed that the alterations and resilience of intestinal microbiota to increased water temperature coincided with the recovery of immune function in fish. Our findings extend the understanding of how the intestinal microbiota in aquatic ectotherms respond to increased water temperature, providing important implications for harnessing the potential benefits of host-associated microorganisms to enhance their resilience to climate change.

The gill and gastrointestinal tract are primary entry routes for pathogens. The symbiotic microbiota are essential to the health, nutrition and disease of fish. Though the intestinal microbiota of Nile tilapia (Oreochromis niloticus) has been extensively studied, information on the mucosa-associated microbiota of this species, especially the gill and gastrointestinal mucosa-associated microbiota, is lacking. This study aimed to characterize the gill and gastrointestinal mucosa- and digesta-associated microbiota, as well as the intestinal metabolite profiles in the New Genetically Improved Farmed Tilapia (NEW GIFT) strain of farmed adult Nile tilapia by high-throughput sequencing and gas chromatography/mass spectrometry metabolomics. The diversity, structure, composition, and predicted function of gastrointestinal microbiota were significantly different across gastrointestinal regions and sample types (Welch t-test; p < 0.05). By comparing the mucosa- and digesta-associated microbiota, linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that Pelomonas, Ralstoniapickettii, Comamonadaceae, and Staphylococcus were significantly enriched in the mucosa-associated microbiota, whereas many bacterial taxa were significantly enriched in the digesta-associated microbiota, including Chitinophagaceae, Cetobacterium, CandidatusCompetibacter, Methyloparacoccus, and chloroplast (LDA score > 3.5). Furthermore, Undibacterium, Escherichia-Shigella, Paeniclostridium, and Cetobacterium were dominant in the intestinal contents and mucosae, whereas Sphingomonasaquatilis and Roseomonasgilardii were commonly found in the gill and stomach mucosae. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analysis revealed that the predictive function of digesta-associated microbiota significantly differed from that of mucosa-associated microbiota (R = 0.8152, p = 0.0001). In addition, our results showed a significant interdependence between specific intestinal microbes and metabolites. Notably, the relative abundance values of several potentially beneficial microbes, including Undibacterium, Crenothrix, and Cetobacterium, were positively correlated with most intestinal metabolites, whereas the relative abundance values of some potential opportunistic pathogens, including Acinetobacter, Mycobacterium, Escherichia-Shigella, Paeniclostridium, Aeromonas, and Clostridiumsensustricto 1, were negatively correlated with most intestinal metabolites. This study revealed the characteristics of gill and gastrointestinal mucosa-associated and digesta-associated microbiota of farmed Nile tilapia and identified a close correlation between intestinal microbes and metabolites. The results serve as a basis for the effective application of targeted probiotics or prebiotics in the diet to regulate the nutrition and health of farmed tilapia.

Psittacosis, also known as parrot fever, is an uncommon infectious disease caused by (C. psittaci). While infections are usually not life-threatening, the pathogenesis and associated complications are not yet fully understood. A 54-year-old male was hospitalized due to a cough, accompanied by expectoration and dyspnea. After admission, the patient's breathing rapidly deteriorated, and despite the use of a ventilator, it was challenging to maintain respiratory function. While initiating extracorporeal membrane oxygenation (ECMO) and empirical anti-infection treatments, the alveolar lavage fluid was collected and examined by metagenomics next generation sequencing (mNGS). The mNGS result indicated . Subsequently, the anti-infection regimen was immediately adjusted. The respiratory function improved on the 13th day after admission, and ECMO was withdrawn. However, the patient developed abdominal distension and intestinal edema. After intravenous infusion therapy, intestinal ischemia and necrosis occurred and surgical resection was performed. The patient's condition improved after the operation and he was transferred to a local hospital for rehabilitation. This case report demonstrates the development of intestinal ischemic necrosis following severe pneumonia. This unique association has not been reported previously and highlights the importance of potential gastrointestinal complications in severe pneumonia, which are often underestimated. Timely diagnoses and treatments of such infections and complications are necessary to achieve favorable clinical outcomes.

Background After millions of years of coevolution, symbiotic microbiota has become an integral part of the host and plays an important role in host immunity, metabolism, and health. Vaccination, as an effective means of preventing infectious diseases, has been playing a vital role in the prevention and control of human and animal diseases for decades. However, so far, minimal is known about the effect of vaccination on fish symbiotic microbiota, especially mucosal microbiota, and its correlation with intestinal metabolism remains unclear. Methods Here we reported the effect of an inactivated bivalent Aeromonas hydrophila / Aeromonas veronii vaccine on the symbiotic microbiota and its correlation with the intestinal metabolism of farmed adult Nile tilapia ( Oreochromis niloticus ) by 16S rRNA gene high-throughput sequencing and gas chromatography-mass spectrometry metabolomics. Results Results showed that vaccination significantly changed the structure, composition, and predictive function of intestinal mucosal microbiota but did not significantly affect the symbiotic microbiota of other sites including gill mucosae, stomach contents, and stomach mucosae. Moreover, vaccination significantly reduced the relative abundance values of potential opportunistic pathogens such as Aeromonas , Escherichia – Shigella , and Acinetobacter in intestinal mucosae. Combined with the enhancement of immune function after vaccination, inactivated bivalent Aeromonas vaccination had a protective effect against the intestinal pathogen infection of tilapia. In addition, the metabolite differential analysis showed that vaccination significantly increased the concentrations of carbohydrate-related metabolites such as lactic acid, succinic acid, and gluconic acid but significantly decreased the concentrations of multiple lipid-related metabolites in tilapia intestines. Vaccination affected the intestinal metabolism of tilapia, which was further verified by the predictive function of intestinal microbiota. Furthermore, the correlation analyses showed that most of the intestinal differential microorganisms were significantly correlated with intestinal differential metabolites after vaccination, confirming that the effect of vaccination on intestinal metabolism was closely related to the intestinal microbiota. Conclusions In conclusion, this paper revealed the microbial and metabolic responses induced by inactivated vaccination, suggesting that intestinal microbiota might mediate the effect of vaccination on the intestinal metabolism of tilapia. It expanded the novel understanding of vaccine protective mechanisms from microbial and metabolic perspectives, providing important implications for the potential influence of vaccination on human intestinal microbiota and metabolism. -tufGxbkxhm-UiFTxxYHNi Video Abstract

Symbiotic microorganisms in the digestive and circulatory systems are found in various crustaceans, and their essential roles in crustacean health, nutrition, and disease have attracted considerable interest. Although the intestinal microbiota of the Chinese mitten crab (Eriocheir sinensis) has been extensively studied, information on the symbiotic microbiota at various sites of this aquatic economic species, particularly the hepatopancreas and hemolymph, is lacking. This study aimed to comprehensively characterize the hemolymph, hepatopancreas, and intestinal microbiota of Chinese mitten crab through the high-throughput sequencing of the 16S rRNA gene. Results showed no significant difference in microbial diversity between the hemolymph and hepatopancreas (Welch t-test; p > 0.05), but their microbial diversity was significantly higher than that in the intestine (p < 0.05). Distinct differences were found in the structure, composition, and predicted function of the symbiotic microbiota at these sites. At the phylum level, the hemolymph and hepatopancreas microbiota were dominated by Proteobacteria, Firmicutes, and Acidobacteriota, followed by Bacteroidota and Actinobacteriota, whereas the gut microbiota was mainly composed of Firmicutes, Proteobacteria, and Bacteroidota. At the genus level, Candidatus Hepatoplasma, Shewanella, and Aeromonas were dominant in the hepatopancreas; Candidatus Bacilloplasma, Roseimarinus, and Vibrio were dominant in the intestine; Enterobacter, norank_Vicinamibacterales, and Pseudomonas were relatively high-abundance genera in the hemolymph. The composition and abundance of symbiotic microbiota in the hemolymph and hepatopancreas were extremely similar (p > 0.05), and no significant difference in functional prediction was found (p > 0.05). Comparing the hemolymph in the intestine and hepatopancreas, the hemolymph had lower variation in bacterial composition among individuals, having a more uniform abundance of major bacterial taxa, a smaller coefficient of variation, and the highest proportion of shared genera. Network complexity varied greatly among the three sites. The hepatopancreas microbiota was the most complex, followed by the hemolymph microbiota, and the intestinal microbiota had the simplest network. This study revealed the taxonomic and functional characteristics of the hemolymph, hepatopancreas, and gut microbiota in Chinese mitten crab. The results expanded our understanding of the symbiotic microbiota in crustaceans, providing potential indicators for assessing the health status of Chinese mitten crab.

To reveal the changes in the gut microbiota of yellow catfish after being infected by Edwardsiella ictaluri, 16S rRNA gene high-throughput sequencing technology was used to analyze the microbial composition and diversity of the healthy and diseased yellow catfish. The gut microbial richness and diversity of the diseased fish were significantly lower than those of healthy fish. The composition and predicted function of yellow catfish gut microbiota were drastically altered after infection by E. ictaluri. Fusobacteriota, Proteobacteria, and Firmicutes were the predominant bacterial phyla in the gut of the healthy fish, while Proteobacteria was the dominant phylum in the gut of the diseased fish. At the genus level, the gut of healthy fish was dominated by Cetobacterium, Plesiomonas, and Romboutsia, while the gut of diseased fish was overwhelmed by the pathogenic E. ictaluri (99.22 ± 0.85%), and Cetobacterium, Plesiomonas, and Romboutsia disappeared. This is the most characteristic feature of the intestinal microbiota composition of yellow catfish edwardsiellosis. The same sequence of E. ictaluri was detected in the intestine of the healthy fish and the liver and intestine of the diseased fish. The anaerobic and Gram-positive bacteria were significantly decreased, and the digestive system, immune system, and metabolic functions of the gut microbiota were significantly reduced in the diseased fish gut. This may be part of the pathogenesis of fish edwardsiellosis.

The abuse of antibiotics in aquaculture has led to the increasing rate of antibiotic resistance of aquatic bacteria including Aeromonas, which is an increasing threat to environmental and human health. To date, no epidemiological cut-off values (COWT) for Aeromonas spp. have been established by the Clinical and Laboratory Standards Institute nor the European Commission on Antimicrobial Susceptibility Testing. In this study, commercially prepared minimum inhibitory concentration (MIC) test 96-well plates (dry-form plates) were used to determine the MIC of eight antimicrobial agents against 556 Aeromonas strains. The obtained MIC distributions were simulated and analyzed by NRI and ECOFFinder to obtain tentative COWT values for Aeromonas spp. The COWT values of eight kinds of representative antimicrobial agents including trimethoprim–sulfamethoxazole, erythromycin, doxycycline, neomycin, colistin, florfenicol, enrofloxacin, and ceftazidime for Aeromonas spp. were established and were 0.25, 64/32, 4/2, 8, 4, 1, 0.062/0.125, and 0.5 μg/mL, respectively. Results showed that Aeromonas spp. had a very high proportion of non-wild-type strains to enrofloxacin, florfenicol, and doxycycline, which are the most widely used antimicrobials in aquaculture. The COWT values for Aeromonas spp. obtained in this study can contribute to the final establishment of COWT for Aeromonas spp. internationally.

Bacterial community plays a key role in environmental and ecological processes of river ecosystems. Given the special climatic and geographical conditions, studying the compositional characteristics of microorganisms in highland rivers and the relationship between such microorganisms and water physicochemical factors is important for an in-depth understanding of microbial ecological mechanisms. In the present study, high-throughput sequencing was used to investigate and study the bacterioplankton community of the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau. The results showed that the Huangshui River had significantly lower alpha diversity than the plain rivers. Despite the similarity in their environmental conditions, the main taxonomic compositions of the bacterial communities were distinct between the Huangshui River and polar regions (the Arctic and Antarctica). Proteobacteria accounted for the largest proportion (30.79–99.98%) of all the sequences, followed by Firmicutes (0–49.38%). Acidiphilium was the most numerous genera, which accounted for 0.03–86.16% of the assigned 16S reads, followed by Acidocella (0–95.9%), both belonging to Alphaproteobacteria. The diverse taxa of potential pathogens, such as Acinetobacter, Pseudomonas, and Aeromonas, were also identified. A principal coordinates analysis, coupled with a canonical correspondence analysis, showed spatial variations in the bacterial community composition. The water physical properties (e.g., Cr6+, total phosphorus, and CODMn); altitude; and land use (e.g., urban land cover and aquaculture) determined the distribution of the bacterioplankton composition. PICRUSt2 revealed that the overall functional profiles of the bacterial communities in different samples were similar, and our results suggested the potential health risks of water sources in this area. This work provided valuable insight into the composition of the plankton bacterial community and its relationship with the environmental factors in the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau and a theoretical foundation for ecological health management.

Increasing attention has been attracted to host microbiota, due to their vital impact on host health. Little is known about the microbiota of the Chinese giant salamander (Andrias davidianus), in spite of the high economic and scientific value of this endangered species. This study was designed to characterise and compare the gut and lung prokaryotic communities of the Chinese giant salamander by high-throughput sequencing. Our study showed that the giant salamander had a lung prokaryotic community that clustered separately from its intestinal microbiota. Statistical analysis (LEfSe) revealed that the bacterial populations were dominated by Geobacter, Sulfurimonas, and Dechloromonas from Proteobacteria phylum, and Corynebacterium from Actinobacteria phylum in the lung, while Parabacteroides, Bacteroides, and PW3 from Bacteroidetes phylum, and Oscillospira from Firmicutes phylum were predominant in the intestine. A particularly innovative finding was the fairly high abundance of Archaea, especially methanogenic Euryarchaeota. The gut dominant Archaea were Methanocorpusculum and Thermoplasmata vadinCA11, while Methanosaeta and Methanoculleus were the main Archaea in the lung. PICRUSt analysis revealed differentiated functional profiles between the intestinal miacrobiota and the lung microbiota. Specially, some microbial metabolic functions were significantly more active in the intestinal microbiota, while the functional genes involved in infectious diseases were much richer in the lung microbiota. This study characterized the prokaryotic microbial community profiles in the gut and lung of the Chinese giant salamander, providing foundational support for future study seeking to understand microbiota of the giant salamander and the role of its microbiota on infectious diseases.