Dysgonomonas massiliensis sp. nov., a new species isolated from the human gut and its taxonogenomic description

Dysgonomonas mossii Strain Shenzhen WH 0221, a New Member of the Genus Dysgonomonas Isolated from the Blood of a Patient with Diabetic Nephropathy, Exhibits Multiple Antibiotic Resistance

Herein, we present a new bacterial strain isolated from infected blood of a patient with diabetic nephropathy. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry failed to identify the strain. 16S rRNA gene sequencing showed the highest similarity (>99.5%) with genus Dysgonomonas, but the strain could not be distinguished from Dysgonomonas oryzarvi and Dysgonomonas mossii. Whole genome sequencing, followed by phylogenetic analysis and average nucleotide identity (>95%) analysis, confirmed that the new strain represented Dysgonomonas mossii, leading it to be named Dysgonomonas mossii strain Shenzhen WH 0221. Shenzhen WH 0221 was 3.60 Mb with 37.4% GC content. It was Gram-stain negative, facultatively anaerobic, and grown on Columbia agar supplemented with 5% of sheep blood, exhibiting a smooth surface and pinpoint morphology. The morphological characteristics of this strain include a short rod shape without flagella and a size of 0.45-0.55 × 0.95-1.52 μm observed under transmission electron microscopy. The physiological and biochemical features and major cellular fatty acids (characterized by C_14:0 3-OH, C_14:0 9-CH₃, and C_16:0) differed from D. mossii CCUG 43457^T and other members of the genus Dysgonomonas. The isolate was found resistant to most cephalosporins, penicillin, norfloxacin, vancomycin, and chloramphenicol, but was susceptible to meropenem, imipenem, tetracycline, clindamycin, and amoxicillin-clavulanic acid. Genes kdpE, ykkD, cmeB, TLA-3, and vanRM found in its genome are probably associated with multiple antibiotic resistance. Lipopolysaccharides, capsules, and cytolysin may also help to illuminate its potential pathogenicity. This is the first report of a case of sepsis caused by Dysgonomonas mossii, and its pathogenic system was analyzed by whole genome sequencing. IMPORTANCE This study identified a new strain, Dysgonomonas mossii strain Shenzhen WH 0221, which has been first reported to cause sepsis isolated from infected blood of a patient with diabetic nephropathy. Physiological and biochemical characterizations, as well as overall fatty acid profile, distinguish Shenzhen WH 0221 from other species of the same genus. However, limited antibiotics were researched for Dysgonomonas mossii. Seventeen antibiotics spanning at least 6 classes were studied, providing a valuable guide to the clinical usage of drugs to treat Dysgonomonas mossii infection. For the first time, we report genome-based functional predictions for Dysgonomonas mossii. Five antibiotic resistance ontologies and more than 200 virulence factors likely underlie the multidrug resistance of Shenzhen WH 0221 and its potential pathogenicity.

Corpse decomposition increases the diversity and abundance of antibiotic resistance genes in different soil types in a fish model

As a common natural phenomenon, corpse decomposition may lead to serious environmental pollution such as nitrogen pollution. However, less is known about antibiotic resistance genes (ARGs), an emerging contaminant, during corpse degradation. Here, ARGs and microbiome in three soil types (black, red and yellow soil) have been investigated between experimental and control groups based on next-generation sequencing and high-throughput quantitative PCR techniques. We found that the absolute abundance of total ARGs and mobile genetic elements (MGEs) in the experimental groups were respectively enriched 536.96 and 240.60 times in different soil types, and the number of ARGs in experimental groups was 7-25 more than that in control groups. For experimental groups, the distribution of ARGs was distinct in different soil types, but sulfonamide resistance genes were always enriched. Corpse decomposition was a primary determinant for ARGs profiles. Microbiome, NH₄⁺ concentrates and pH also significantly affected ARGs profiles. Nevertheless, soil types had few effects on ARGs. For soil microbiome, some genera were elevated in experimental groups such as the Ignatzschineria and Myroides. The alpha diversity is decreased in experimental groups and microbial community structures are different between treatments. Additionally, the Escherichia and Neisseria were potential pathogens elevated in experimental groups. Network analysis indicated that most of ARGs like sulfonamide and multidrug resistance genes presented strong positively correlations with NH₄⁺ concentrates and pH, and some genera like Ignatzschineria and Dysgonomonas were positively correlated with several ARGs such as aminoglycoside and sulfonamide resistance genes. Our study reveals a law of ARGs' enrichment markedly during corpse decomposing in different soil types, and these ARGs contaminant maintaining in environment may pose a potential threat to environmental safety and human health.

Seramator thermalis gen. nov., sp. nov., a novel cellulose- and xylan-degrading member of the family Dysgonamonadaceae isolated from a hot spring

Two anaerobic bacteria, designated strains SYSU GA16112^T and SYSU GA16107, were isolated from a hot spring in Tengchong County, Yunnan Province, south-west PR China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains SYSU GA16112^T and SYSU GA16107 belong to the family Dysgonamonadaceae. Cells of strains SYSU GA16112^T and SYSU GA16107 were Gram-stain-negative, rod-shaped and non-motile. The major fatty acids (>10 %) of strains SYSU GA16112^T and SYSU GA16107 were identified as anteiso-C_15 : 0 and anteiso-C_17 : 0 3OH. The polar lipid profile of strain SYSU GA16112^T was found to consist of phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phosphoglycolipids, two unidentified aminolipids and one unidentified polar lipid, while that of strain SYSU GA16107 consisted of phosphatidylethanolamine, two unidentified polar lipids, three unidentified aminophospholipids, two unidentified phosphoglycolipids and one unidentified aminolipid. The genomic DNA G+C contents of strains SYSU GA16112^T and SYSU GA16107 were determined to be 41.90 and 41.89 %, respectively, and the average nucleotide identity value between them was 99.99 %. Based on their morphological and physiological properties, and results of phylogenetic analyses, strains SYSU GA16112^T and SYSU GA16107 are considered to represent a novel species of a novel genus, for which the name Seramator thermalis gen. nov., sp. nov. (type strain SYSU GA16112^T=CGMCC 1.5281^T=KCTC 15753^T) is proposed.

Development and application of aerobic, chemically defined media for Dysgonomonas

Members of Dysgonomonas are Gram-stain-negative, non-motile, facultatively anaerobic coccobacilli originally described in relation to their isolation from stool and wounds of human patients (CDC group DF-3). More recently, Dysgonomonas have been found to be widely distributed in terrestrial environments and are particularly enriched in insect systems. Their prevalence in xylophagous insects such as termites and wood-feeding cockroaches, as well as in soil-fed microbial fuel cells, elicit interest in lignocellulose degradation and biofuel production, respectively. Their occurrence in mosquito and fruit fly have implications relating to symbiosis, host immunology and developmental biology. Additionally, their presence in termite, mosquito and nematode present novel opportunities for pest and vector control. Currently, the absolute growth requirements of Dysgonomonas are unknown, and they are commonly cultured under anaerobic conditions on complex media containing blood, peptones, tryptones, and yeast, plant or meat extracts. Restrictive and undefined culturing conditions preclude physiological and genetic studies, and thus further understanding of their metabolic potential. Here we describe the requirements for growth of termite-derived Dysgonomonas isolates and create parallel complex, defined and minimal media that permit vigorous and reliable aerobic growth. Furthermore, we show that these media can be used to easily enrich for Dysgonomonas isolates from densely-colonized and microbially-diverse environmental samples.

Changes in syntrophic microbial communities, EPS matrix, and gene-expression patterns in biofilm anode in response to silver nanoparticles exposure

Understanding the toxic effect of silver nanoparticles (AgNPs) on various biological wastewater treatment systems is of significant interest to researchers. In recent years, microbial electrochemical technologies have opened up new opportunities for bioenergy and chemicals production from organic wastewater. However, the effects of AgNPs on microbial electrochemical systems are yet to be understood fully. Notably, no studies have investigated the impact of AgNPs on a microbial electrochemical system fed with a complex fermentable substrate. Here, we investigated the impact of AgNPs (50 mg/L) exposure to a biofilm anode in a microbial electrolysis cell (MEC) fed with glucose. The volumetric current density was 29 ± 2.0 A/m³ before the AgNPs exposure, which decreased to 20 ± 2.2 A/m³ after AgNPs exposure. The biofilms produced more extracellular polymeric substances (EPS) to cope with the AgNPs exposure, while carbohydrate to protein ratio in EPS considerably increased from 0.4 to 0.7. Scanning electron microscope (SEM) imaging also confirmed the marked excretion of EPS, forming a thick layer covering the anode biofilms after AgNPs injection. Transmission electron microscope (TEM) imaging showed that AgNPs still penetrated some microbial cells, which could explain the deterioration of MEC performance after AgNPs exposure. The relative expression level of the quorum signalling gene (LuxR) increased by 30%. Microbial community analyses suggested that various fermentative bacterial species (e.g., Bacteroides, Synergistaceae_vadinCA02, Dysgonomonas, etc.) were susceptible to AgNPs toxicity, which led to the disruption of their syntrophic partnership with electroactive bacteria. The abundance of some specific electroactive bacteria (e.g., Geobacter species) also decreased. Moreover, decreased relative expressions of various extracellular electron transfer associated genes (omcB, omcC, omcE, omcZ, omcS, and pilA) were observed. However, the members of family Enterobacteriaceae, known to perform a dual function of fermentation and anodic respiration, became dominant after biofilm anode exposed to AgNPs. Thus, EPS extraction provided partial protection against AgNPs exposure.