Genome sequence of the 17β-estradiol-utilizing bacterium Sphingomonas strain KC8

Hormonal Environment Shapes the Oral Microbiome

Hormones are present in oral fluids and undergo dynamic changes throughout life. Hormonal changes can influence the interactions between the microbial community and the host. The oral microbiome is sensitive to changes in the oral environment, and hormonal fluctuations can create conditions that favour the growth of certain types of bacteria over others. Since the gingival niche harbours the resident microbial community in the biofilm form, while saliva has a transient microbiota in the planktonic form, both could modulate the host-microbial interaction under hormonal oscillations.The microbiome and hormones have a dynamic bidirectional interaction. Specific oral microorganisms can metabolize steroid hormones, disrupting their host regulation. Hormones can serve as host-microbial crosstalk related to health and disease. Hormonal imbalances are associated with systemic diseases such as polycystic ovary syndrome, endometriosis, cortisol-related conditions and oral cancer. Elucidating the complex relationship between steroid hormones and the oral microbiome offers valuable insights into the mechanisms of the disease and potential therapeutic avenues for maintaining oral and systemic health.

Heterogeneity of the Tissue-specific Mucosal Microbiome of Normal Grass Carp (Ctenopharyngodon idella)

Microbiome plays key roles in the digestion, metabolism, and immunity of the grass carp (Ctenopharyngodon idella). Here, we characterized the normal microbiome of the intestinal contents (IC), skin mucus (SM), oral mucosa (OM), and gill mucosa (GM) of the grass carp, as well as the microbiome of the sidewall (SW) of the raising pool, using full-length 16S rRNA sequencing based on the PacBio platform in this specie for the first time. Twenty phyla, 38 classes, 130 families, 219 genera, and 291 species were classified. One hundred four common classified species might be core microbiota of grass carp. Proteobacteria, Bacteroides, and Cyanobacteria were the dominant phyla in the niche of grass carp. Proteobacteria and Bacteroides dominated the taxonomic composition in the SM, GM, and OM, while Proteobacteria, Planctomycetota, and Cyanobacteria preponderated in the IC and SW groups. Microbiota of IC exhibited higher alpha diversity indices. The microbial communities clustered either in SW or the niche from grass carp, significantly tighter in the SW, based on Bray-Curtis distances (P < 0.05). SM, GM, and OM were similar in microbial composition but were significantly different from IC and SW, while IC had similarity with SW due to their common Cyanobacteria (P < 0.05). Differences were also reflected by niche-specific and differentially abundant microorganisms such as Noviherbaspirillum in the SM and Rhodopseudomonas palustris, Mycobacterium fortuitum, and Acinetobacter schindleri in GM. Significantly raised gene expression was found in IC and SM associated with cell cycle control, cell division, chromosome, coenzyme transport and metabolism, replication, recombination and repair, cell motility, post-translational modification, signal transduction mechanisms, intracellular trafficking, secretion, and vesicles by PICRUSt. This work may be of great value for understanding of fish-microbial co-workshops, especially in different niche of grass carp.

Genomic analysis of Gordonia polyisoprenivorans strain R9, a highly effective 17 beta-estradiol- and steroid-degrading bacterium

The increasing levels of estrogens and pollution by other steroids pose considerable challenges to the environment. In this study, the genome of Gordonia polyisoprenivorans strain R9, one of the most effective 17 beta-estradiol- and steroid-degrading bacteria, was sequenced and annotated. The circular chromosome of G. polyisoprenivorans R9 was 6,033,879 bp in size, with an average GC content of 66.91%. More so, 5213 putative protein-coding sequences, 9 rRNA, 49 tRNA, and 3 sRNA genes were predicted. The core-pan gene evolutionary tree for the genus Gordonia showed that G. polyisoprenivorans R9 is clustered with G. polyisoprenivorans VH2 and G. polyisoprenivorans C, with 93.75% and 93.8% similarity to these two strains, respectively. Altogether, the three G. polyisoprenivorans strains contained 3890 core gene clusters. Strain R9 contained 785 specific gene clusters, while 501 and 474 specific gene clusters were identified in strains VH2 and C, respectively. Furthermore, whole genome analysis revealed the existence of the steroids and estrogens degradation pathway in the core genome of all three G. polyisoprenivorans strains, although the G. polyisoprenivorans R9 genome contained more specific estrogen and steroid degradation genes. In strain R9, 207 ABC transporters, 95 short-chain dehydrogenases (SDRs), 26 monooxygenases, 21 dioxygenases, 7 aromatic ring-hydroxylating dioxygenases, and 3 CoA esters were identified, and these are very important for estrogen and steroid transport, and degradation. The results of this study could enhance our understanding of the role of G. polyisoprenivorans R9 in estradiol and steroid degradation as well as evolution within the G. polyisoprenivorans species.

Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557

Rhodococcus equi ATCC13557 was selected as a model organism to study oestrogen degradation based on its previous ability to degrade 17α-ethinylestradiol (EE2). Biodegradation experiments revealed that R. equi ATCC13557 was unable to metabolise EE2. However, it was able to metabolise E2 with the major metabolite being E1 with no further degradation of E1. However, the conversion of E2 into E1 was incomplete, with 11.2 and 50.6% of E2 degraded in mixed (E1-E2-EE2) and E2-only conditions, respectively. Therefore, the metabolic pathway of E2 degradation by R. equi ATCC13557 may have two possible pathways. The genome of R. equi ATCC13557 was sequenced, assembled, and mapped for the first time. The genome analysis allowed the identification of genes possibly responsible for the observed biodegradation characteristics of R. equi ATCC13557. Several genes within R. equi ATCC13557 are similar, but not identical in sequence, to those identified within the genomes of other oestrogen degrading bacteria, including Pseudomonas putida strain SJTE-1 and Sphingomonas strain KC8. Homologous gene sequences coding for enzymes potentially involved in oestrogen degradation, most commonly a cytochrome P450 monooxygenase (oecB), extradiol dioxygenase (oecC), and 17β-hydroxysteroid dehydrogenase (oecA), were identified within the genome of R. equi ATCC13557. These searches also revealed a gene cluster potentially coding for enzymes involved in steroid/oestrogen degradation; 3-carboxyethylcatechol 2,3-dioxygenase, 2-hydroxymuconic semialdehyde hydrolase, 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase, 3-(3-hydroxy-phenyl)propionate hydroxylase, cytochrome P450 monooxygenase, and 3-oxosteroid 1-dehydrogenase. Further, the searches revealed steroid hormone metabolism gene clusters from the 9, 10-seco pathway, therefore R. equi ATCC13557 also has the potential to metabolise other steroid hormones such as cholesterol.

Effects of carbon sources on 17 beta-estradiol degradation by Sphingomonas sp. and the analysis of the involved intracellular metabolomics

17β-estradiol (E2) ubiquitously exists in various water bodies with long-term endocrine-disrupting and carcinogenic impacts on wildlife even at the trace level of ng L^-1. However, it remains unclear how easy-to-degrade carbon sources alter E2 biodegradation patterns. In this study, E2 biodegradation by Sphingomonas sp. MCCC 1A06484 was investigated with regard to alternative carbon sources. Results showed that the bacterium preferentially utilized glucose, sodium succinate and sodium acetate over E2. Interestingly, the presence of these preferred nutrients increased the E2 removal efficiency by 20.1%. Furthermore, a positive relation (p < 0.05) between the utilization of total organic carbon (TOC) and E2 was found. Using intracellular metabolomics by UHPLC-QTOF-MS, 11 up-regulated and 35 down-regulated metabolites (variable importance > 1, p < 0.05) were identified in the bacterium when cultivated with E2 under various carbon and nitrogen backgrounds. The E2 exposure contributed to metabolism changes of lipid, nucleotide, carbohydrate, amino acid and membrane transport, which were considered to play roles in the E2 metabolism. The up-regulated phosphatidylcholine might act as an indicator during the bacterial degradation of E2. Generally, this study contributes to an in-depth understanding of E2 biodegradation in complex environments with multiple carbon and nitrogen sources.

Draft Genome Sequence of Triclosan-Degrading Bacterium Sphingomonas sp. Strain YL-JM2C, Isolated from a Wastewater Treatment Plant in China

Sphingomonas sp. strain YL-JM2C was isolated from a wastewater treatment plant in Xiamen, China, by enrichment on triclosan. The bacterium is of special interest because of its ability to degrade triclosan. Here, we present a draft genome sequence of the microorganism and its functional annotation. To our best knowledge, this is the first report of a draft genome sequence of a triclosan-degrading bacterium

Draft Genome Sequence of the Bisphenol A-Degrading Bacterium Sphingobium sp. Strain YL23

Sphingobium sp. strain YL23, a novel bacterium isolated from sewage sludge of a domestic wastewater treatment plant, has been shown to completely degrade bisphenol A under aerobic conditions. Here, we describe a 3.8-Mb assembly of its genome sequence and major findings from its annotation.

Microbial degradation of steroidal estrogens

Steroidal estrogens, widespread in the environment, are contaminants of potential concern because exposure to these compounds can cause adverse impacts on aquatic life. Intensive research efforts have been undertaken in order to better understand the environmental occurrence of these compounds. In addition to physical/chemical reactions, biological processes - microbial biodegradation of steroidal estrogens - play a vital role in determining the fate and transport of these compounds in built and natural environments. This review summarizes the current state of knowledge on the microbiology of estrogen biodegradation. Aerobic and anaerobic estrogen-degrading microorganisms are phylogenetically diverse; they are mainly isolated from soils, activated sludge, dental plaque and intestines. Estrogens can be degraded via growth-linked and non-growth-linked reactions, as well as through abiotic degradation in the presence of selective microorganisms. Current knowledge on estrogen biodegradation kinetics and pathways is limited. Molecular methods are useful in deciphering estrogen-degrading microbial community and tracking the quantity of known degraders in bioreactors with different operating conditions. Future research efforts aimed at bridging knowledge gaps on estrogen biodegradation are also proposed.

Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities

Sphingomonads comprise a physiologically versatile group within the Alphaproteobacteria that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that Sphingomonas, Sphingobium, Sphingopyxis, and Novosphingobium are well-resolved monophyletic groups with the exception of Sphingomonas sp. strain SKA58, which we propose belongs to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.

Role of sex steroid hormones in bacterial-host interactions

Sex steroid hormones play important physiological roles in reproductive and nonreproductive tissues, including immune cells. These hormones exert their functions by binding to either specific intracellular receptors that act as ligand-dependent transcription factors or membrane receptors that stimulate several signal transduction pathways. The elevated susceptibility of males to bacterial infections can be related to the usually lower immune responses presented in males as compared to females. This dimorphic sex difference is mainly due to the differential modulation of the immune system by sex steroid hormones through the control of proinflammatory and anti-inflammatory cytokines expression, as well as Toll-like receptors (TLRs) expression and antibody production. Besides, sex hormones can also affect the metabolism, growth, or virulence of pathogenic bacteria. In turn, pathogenic, microbiota, and environmental bacteria are able to metabolize and degrade steroid hormones and their related compounds. All these data suggest that sex steroid hormones play a key role in the modulation of bacterial-host interactions.