Streptococcus agalactiae (S. agalactiae), also known as group B Streptococcus (GBS), is an important pathogen for neonatal pneumonia, meningitis, bovine mastitis, and fish meningoencephalitis. The global outbreaks of Streptococcus disease in tilapia cause huge economic losses and threaten human food hygiene safety as well. To investigate the mechanism of S. agalactiae pathogenesis in tilapia and develop attenuated S. agalactiae vaccine, this study sequenced and comparatively analyzed the whole genomes of virulent wild-type S. agalactiae strain HN016 and its highly-passaged attenuated strain YM001 derived from tilapia. We performed Illumina sequencing of DNA prepared from strain HN016 and YM001. Sequencedreads were assembled and nucleotide comparisons, single nucleotide polymorphism (SNP) , indels were analyzed between the draft genomes of HN016 and YM001. Clustered regularly interspaced short palindromic repeats (CRISPRs) and prophage were detected and analyzed in different S. agalactiae strains. The genome of S. agalactiae YM001 was 2,047,957 bp with a GC content of 35.61 %; it contained 2044 genes and 88 RNAs. Meanwhile, the genome of S. agalactiae HN016 was 2,064,722 bp with a GC content of 35.66 %; it had 2063 genes and 101 RNAs. Comparative genome analysis indicated that compared with HN016, YM001 genome had two significant large deletions, at the sizes of 5832 and 11,116 bp respectively, resulting in the deletion of three rRNA and ten tRNA genes, as well as the deletion and functional damage of ten genes related to metabolism, transport, growth, anti-stress, etc. Besides these two large deletions, other ten deletions and 28 single nucleotide variations (SNVs) were also identified, mainly affecting the metabolism- and growth-related genes. The genome of attenuated S. agalactiae YM001 showed significant variations, resulting in the deletion of 10 functional genes, compared to the parental pathogenic strain HN016. The deleted and mutated functional genes all encode metabolism- and growth-related proteins, not the known virulence proteins, indicating that the metabolism- and growth-related genes are important for the pathogenesis of S. agalactiae.

In aquaculture, the use of probiotics to improve growth, immunity, and stress resistance in crustaceans has gained increasing attention. This study examined the effects of incorporating different levels of Rhodotorula mucilaginosa (0.0, 0.1, 1.0, and 10.0 g/kg) into the diet on growth performance, antioxidant capacity (AOC), immune function, Toll/Imd, and JAK‐STAT signaling pathways in red claw crayfish ( Cherax quadricanatus ). The investigation was conducted through a 56‐day feeding trial. The main results are as follows: Compared with the control group (0.0 g/kg), different R. mucilaginosa levels significantly increased ( p < 0.05) the specific growth rate (SGR) and weight gain rate (WGR) of red claw crayfish, significantly increased ( p < 0.05) the activities of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX), glutathione S‐transferase (GST), total AOC (T‐AOC), and acid phosphatase (ACP) in hepatopancreas of red claw crayfish, and significantly upregulated ( p < 0.05) the relative expression levels of tumor necrosis factor receptor‐associated protein 6, akirin, immunodeficiency homolog, interferon regulatory factor 4, Toll‐like receptor (TLR) 6, TLR 2, Janus kinase, signal transducer activator of transcription, tumor necrosis factor α, interleukin‐1β, transforming growth factor‐β1 genes in the hepatopancreas of red claw crayfish. In conclusion, R. mucilaginosa significantly enhanced red claw crayfish’s growth, AOC, and immune function, and activated the Toll/Imd and JAK‐STAT signaling pathways. In this experimental context, the ideal addition level of R. mucilaginosa is 1.0 g/kg.

The growth environment significantly influences the intestinal microbiota of aquatic organisms. We investigated the composition and functional differences in the intestinal microbiota of red claw crayfish (Cherax quadricarinatus) in rice fields (RB) and ponds (PB) by 16S rDNA high-throughput sequencing technology. The results indicate that the Shannon, Simpson, Sobs, Chao1, and ACE indices of PB are all higher than those of RB, demonstrating greater diversity and richness of intestinal microbiota. The dominant phyla in the intestinal microbiota of the Cherax quadricarinatus were Proteobacteria, Tenericutes, and Firmicutes. Tenericutes and Proteobacteria were significantly more abundant in the RB than in the PB, while Planctomycetes and Firmicutes were significantly more abundant in the PB than in the RB. The results of network correlation analysis indicate that Proteobacteria and Firmicutes exhibit strong connectivity with other microbial groups in the gut microbiota of Cherax quadricarinatus, showing significant centrality. They play an important role in the interactions within the gut microbiota community. The dominant bacterial genera in the Cherax quadricarinatus’s gut were Citrobacter, Candidatus_Bacilloplasma, and Clostridium_sensu_stricto_1. The abundance of the genus Clostridium was significantly higher in the PB than in the RB, whereas the abundance of Candidatus_Hepatoplasma and Vibrio was significantly lower in the PB than in the RB. The prediction function of KEGG enrichment showed that the abundance of Amino acid metabolism, Biosynthesis of Other Secondary Metabolites, Transport and Catabolism, Cancers, and Nervous System, Substance Dependence were significantly higher in the PB, while the infectious diseases pathway was enriched in the RB. In summary, our results revealed significant differences in the composition and diversity of intestinal microbiota in the Cherax quadricarinatus between rice paddy and pond farming environments. The intestinal microbiota of the Cherax quadricarinatus grown in pond environments exhibit higher diversity and stability, manifested by an increase in beneficial bacteria abundance and a decrease in opportunistic pathogens. These findings significantly improve understanding of the complex relationship among Cherax quadricarinatus, intestinal microbiota, and the environment.

Streptococcus agalactiae (Group B Streptococcus, GBS) is a common bacteria species infecting both human and bovine. Previous studies have shown that the GBS isolated from human and bovine are mostly unrelated and belong to separate populations. However, recently, the bovine GBS CC103 has become the dominant epidemic strain and frequently isolated from human patients. In particular, the ST485 GBS, a member of CC103, has become the new dominant ST in China and exhibited very high pathogenicity. This phenomenon is not consistent with the established understanding about the relationship between bovine and human GBS, which needs to be re-investigated. The genome-based phylogenetic analysis showed that the human and bovine GBS CC103 strains had very close genetic relationship and they were alternately distributed on the evolutionary tree. CC103 strains evolved into several branches, including the ST485, which exhibited high pathogenicity and specifically infected human. Compared to other CC103 strains, the ST485 lacked Lac.2 gene structure and acquired the CadDX gene structure in their genomes. Our results indicate that GBS CC103 could propagate across human and bovine, and GBS ST485 might evolve from the ST103 that could infect both human and bovine. Moreover, the recombination of Lac.2 and CadDX gene structures might play an important role in the formation of highly pathogenic ST485 in China.

The giant freshwater prawn (GFP; Macrobrachium rosenbergii), a tropical species cultured worldwide, has high market demand and economic value. Male GFP growth varies considerably; however, the mechanisms underlying these growth differences remain unclear. In this study, we collected gut and hemolymphatic samples of large (ML), medium (MM), and small (MS) male GFPs and used the 16S rRNA sequencing and liquid chromatography–mass spectrometry-based metabolomic methods to explore gut microbiota and metabolites associated with GFP growth. The dominant bacteria were Firmicutes and Proteobacteria; higher growth rates correlated with a higher Firmicutes/Bacteroides ratio. Serum metabolite levels significantly differed between the ML and MS groups. We also combined transcriptomics with integrative multiomic techniques to further elucidate systematic molecular mechanisms in the GFPs. The results revealed that Faecalibacterium and Roseburia may improve gut health in GFP through butyrate release, affecting physiological homeostasis and leading to metabolic variations related to GFP growth differences. Notably, our results provide novel, fundamental insights into the molecular networks connecting various genes, metabolites, microbes, and phenotypes in GFPs, facilitating the elucidation of differential growth mechanisms in GFPs.