Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species

Paracoccus yibinensis sp. nov., a novel bacterium with astaxanthin producing isolated from the environment of Chinese distilled Baijiu

An aerobic, Gram-stain-negative bacterium, designated as strain WLY502T, was isolated from the environment of Baobaoqu starter production. The strain was with a short rod shape cells 0.5-0.7 μm wide and 1.1-2.0 μm long, arranged singly or in pairs. The isolate was able to grow at temperatures of 20-37 °C (optimum growth at 25 °C), at pH 5.0-10.0 (optimum growth at pH 7.0) and in the presence of 0-5% (w/v) NaCl (optimum growth with 0% NaCl). Ribose, xylose, arabinose, mannose, glucose and galactose were the major cell-wall sugar. The meso-diaminopimelic acid (meso-DAP) was the diagnostic amino acid. The main polar lipids of strain WLY502T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), unidentified aminolipids (UAL 1-2), unidentified aminophospholipid (UAPL), unidentified aminophospholipid (UAPL), unidentified phospholipid (UPL), unidentified lipids (UL 1-5), glycolipid (GL). Ubiquinone Q-10 was predominant menaquinone and C18:1 ω7c (80.5%) was the major fatty acid. Comparisons of 16S rRNA gene sequence indicated that strain WLY502T was most closely related to Paracoccus acridae SCU-M53T (98.48%), Paracoccus haematequi M1-83T (98.40%). The average nucleotide identity (ANI) values strain WLY502T and the two type strains mentioned above were 91.19% and 70.96%. The average amino identity (AAI) value between them were 93.42% and 87.19%. Additionally, the digital DNA-DNA hybridization (dDDH) value between them is 42.9% and 30.1%. The genomic DNA G + C content was 64.99%. Strain WLY502T could produce astaxanthin and contains several genes (such as MalK, UgpE, UgpA, PRK07067, PBP2 TMBP ike, YcjU, YjiC, crtI-fam, crtY, ERG9, and IspA) involved in astaxanthin. Therefore, strain WLY502T may have development and utilisation value in flavouring agents. Based on the evidence presented, strain WLY502T (CICC 25237T = JCM 36429T) is proposed as the type strain of a novel species, designated as Paracoccus yibinensis sp. nov.

Trujillonella humicola sp. nov., a siderophore-synthesizing bacterium isolated from black soil in Northeast China

A Gram-stain-positive, motile, and oval-shaped bacterium, designated as SYSU BS000539T, was isolated from black soil in Heilongjiang Province, China. 16S rRNA gene sequencing revealed that the isolate shared the highest similarity to Trujillonella endophytica DSM 45413T (98.32%), and phylogenetic analysis confirmed that it belonged to the genus Trujillonella. The strain could grow at temperatures from 15 to 37 °C (with an optimum at 28 °C), in salt concentrations of 0-5% (w/v) (with an optimum at 0%), and at pH levels from 6.0 to 10.0 (with an optimum at 8.0). The dominant cellular fatty acids (> 5%) were iso-C16:0, iso-C15:0, and iso-C16:1, while the principal respiratory quinones was menaquinone MK-9 (H4) with menaquinone MK-8 as minor components. Polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol methylphosphonolipid, an unidentified aminolipid and two unidentified polar lipids. The G + C content of the genome was 74.97%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SYSU BS000539T and T. endophytica DSM 45413T were 84.10% and 27.60%, respectively, falling below species delineation thresholds. Combining phylogenetic, genotypic, chemotaxonomic, physiological and biochemical analyses, it is evident that SYSU BS000539T represented a novel species within the genus Trujillonella, for which the name Trujillonella humicola sp. nov. is proposed. The type strain of the proposed novel species is SYSU BS000539T (= MCCC 1K09330T = KCTC 59402T).

Impact of altitudinal variations on plant growth dynamics, nutritional composition, and free living rhizospheric N2 fixing bacterial community of Eruca sativa

High-altitude environments present unique abiotic stresses, yet their impact on the growth, nutritional quality, and rhizospheric interactions of E. sativa remains underexplored. Here, we investigate the altitudinal variations in growth dynamics, nutritional composition, and rhizospheric free-living N2-fixing bacteria (NFBs) of E. sativa (Arugula) grown at higher (3,524 m, Leh-Ladakh) and lower (321 m, Chandigarh) altitudes. Results revealed significant physiological adaptations to high-altitude conditions, with increased concentrations of magnesium (748.84 ± 4.06 mg/100 g), iron (189.83 ± 2.16 mg/100 g), and manganese (8.48 ± 0.27 mg/100 g), while potassium (3,400.83 ± 3.82 mg/100 g), sodium (175.83 ± 1.44 mg/100 g), and copper (1.69 ± 0.01 mg/100 g) were higher at lower-altitude. Zinc content remained unchanged. Notably, dietary nitrate was higher (155.67 ± 22.12 mg/100 g) at high-altitudes. Rhizospheric NFBs were isolated and functionally characterized for N2-fixation efficacy along with various plant growth-promoting (PGP) attributes; viz., production of ammonia, siderophores, HCN, IAA and phosphate solubilization. Field inoculation with selected strains significantly enhanced nitrogen content and plant growth. Soil chemical analysis further revealed significant differences between the altitudes. A total of twenty-seven NFBs belonging to Actinobacteria (77%), Proteobacteria (11%), Firmicutes(8%), and Bacteroidetes(4%) were isolated, with Streptomyces being the predominant genus, exhibiting distinct species at different altitudes. Remarkably, high-altitude strains showed significantly higher N2-fixing efficiencies (88.15 ± 17.41 µgN mL-1) than lower-altitude (65.7 ± 14.36 µgN mL-1) along with superior PGP traits. Overall, these findings suggest that E. sativa, enriched in key nutrients at high-altitudes, could be a valuable functional food crop, addressing the dietary needs of high-altitude populations. Furthermore, the rhizospheric NFBs identified in this study may be potentially beneficial for the development of novel bio-fertilizers, promoting eco-friendly agricultural practices through improved N2-fixation. Further field trials are recommended to validate their potential for sustainable crop production.

Genome analysis of manure and soil-dwelling Acinetobacter strains indicates potential health risks associated with antibiotic resistance and virulence factors

The genus Acinetobacter includes opportunistic pathogenic species of increasing clinical importance due to their ability to resist multiple antibiotics and to face multiple environmental stresses. Here, comprehensive whole-genome analysis was used to reveal the presence of genes potentially related to pathogenicity in 11 tetracycline-resistant Acinetobacter isolates from manure of dairy cows under tetracycline and amoxicillin prophylaxis and from soils affected by this manure. The isolates were identified as Acinetobacter pseudolwoffii, A. gerneri, A. gandensis, and A. amyesii and screened their genomes for the presence of genes related to host colonization, infection, or environmental persistence. We detected 164 genes of antimicrobial resistance, virulence factors, mobile genetic elements, or biofilm formation. All isolates were predicted to be human pathogens with high probability (0.7-0.8) and the manure isolates identified as A. pseudolwoffii carried a top-risk human-associated aminoglycoside resistance gene. The phenotypic characterization of the isolates showed that they could all grow at 37 °C, some up to 41 °C, and that they showed differential susceptibility to several antibiotics, with one isolate identified as A. gandensis being multi-resistant. Our analyses suggest that environmental Acinetobacter strains from fresh manure and manured soils possess risky antibiotic-resistance genes and phenotypic traits of clinical relevance indicating potential pathogenicity.

Characterization of Lachnoanaerobaculum sanguinis sp. nov., isolated from a blood culture of an acute myeloid leukemia patient with chemotherapy-related bacteremia

OBJECTIVE

This study was to characterize and determine the classification of the novel strain TM49T, isolated from a blood culture of a patient who developed bacteremia while receiving high-dose cytarabine chemotherapy for acute myeloid leukemia.

METHODS

The novel strain TM49T was characterized at the species level through a polyphasic taxonomic analysis, incorporating morphological, physiological, biochemical, phylogenetic, and genome sequence analyses.

RESULTS

16S rRNA gene sequence analysis revealed that the strain belonged to the genus Lachnoanaerobaculum. The 16S rRNA gene sequence of strain TM49T was observed to be most similar to that of "Lachnoanaerobaculum gingivalis" strain ChDC B114T (99.2 %). Strain TM49T formed circular, glossy, slightly milky colonies with an undulate margin on BD™ Columbia Agar containing 5 % sheep blood after 48 h at 37 °C, exhibiting less spreading compared to species of the genus Lachnoanaerobaculum. The major fatty acids of strain TM49T were C16:0, C14:0, C18:1 ω9c DMA, and C18:1 ω7c DMA. The draft genome sequence of strain TM49T was 2,821,554 bp in length, with a G + C content of 36.4. Digital DNA-DNA hybridization values between strain TM49T and "L. gingivalis" ChDC B114T, L. umeaense CD3: 22T, L. orale N1T, and L. saburreum CCUG 28089T were 52.2 %, 29.7 %, 26.2 %, and 24.5 %, respectively. The Orthologous Average Nucleotide Identity values between strain TM49T and "L. gingivalis" ChDC B114T, L. umeaense CD3: 22T, L. orale N1T, and L. saburreum CCUG 28089T were 93.1 %, 84.9 %, 83.2 %, and 81.5 %, respectively.

CONCLUSION

Strain TM49T (JCM 36186T = DSM 116945T) was found to be distinct from previously described species of the genus Lachnoanaerobaculum. Therefore, it is proposed as a new species, Lachnoanaerobaculum sanguinis sp. Nov., with strain TM49T as the type strain (= JCM 36186T = DSM 116945T).

Excavation of resources of Streptomyces species in frozen soils of the Qinghai-Tibet Plateau based on RpfA protein of Streptomyces coelicolor

This study is aimed at the actual demand for exploring new species resources of Streptomyces, and aims to solve the technical bottleneck of Streptomyces isolation and culture. A new method was established based on the resuscitation function of the RpfA protein from Streptomyces coelicolor CGMCC 4.1658T to isolate unculturable or difficult-to-culture Streptomyces species, and it was applied to explore Streptomyces species resources in special habitats in the frozen soils of the Qinghai-Tibet Plateau. The RpfA protein of S. coelicolor was heterologously expressed and validated for its in vitro activity. The purified RpfA protein was then used to isolate Streptomyces from soil samples in the frozen soils of the Qinghai-Tibet Plateau, followed by an investigation into the impact of the RpfA protein on the cultivability of Streptomyces species. The results showed that the RpfA protein had a significant promoting effect on the germination of spores of both S. coelicolor itself and other species of the Streptomyces genus, and when a suitable concentration of RpfA protein was added to the culture medium, it could significantly improve the culturability of members of phylum Actinomycetota, especially Streptomyces species. In addition, many new species of the genus Streptomyces and other genera of phylum Actinomycetota were discovered. This study provides a new approach for further exploring Streptomyces species resources in special environments such as the Qinghai-Tibet Plateau and developing new biologically active substances produced by Streptomyces.

Flavobacterium anseongense sp. nov. and Flavobacterium wongokense sp. nov., isolated from freshwater and freshwater soil in South Korea

Two novel, non-motile, Gram-stain-negative, rod-shaped bacterial strains, designated AS60T and WG47T, were isolated from freshwater in South Korea. To clarify their taxonomic positions, both strains were characterized based on genomic information, including 16S rRNA gene and draft genome sequences. Phylogenetic analyses revealed that both isolates belong to the genus Flavobacterium. Based on 16S rRNA gene sequencing, AS60T clustered with Flavobacterium silvisoli KACC 21178T (96.09%), Flavobacterium cheonhonense KACC 14967T (96.07%) and Flavobacterium sangjuense KACC 17473T (95.96%). Strain WG47T showed the highest similarity to Flavobacterium dankookense KACC 23179T (97.14%), F. cheonhonense KACC 14967T (97.07%) and Flavobacterium chungnamense KACC 14971T (96.71%). The draft genomes of AS60T and WG47T were 3.07 and 3.30 Mb, with G+C contents of 35.6 and 38.9 mol%, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were calculated. For AS60T, ANI values compared to F. silvisoli KACC 21178T, F. cheonhonense KACC 14967T and WG47T were 76.67, 79.38 and 76.01%, respectively, with dDDH values of 20, 19.6 and 22.1%. For WG47T, ANI values compared to F. dankookense KACC 23179T and F. cheonhonense KACC 14967T were 75.12 and 74.75%, with dDDH values of 19.9 and 19.2%. Both strains exhibited MK-6 as the predominant respiratory quinone, and their fatty acid profiles included iso-C15:1, iso-C15:0 3OH, iso-C15:1 G, iso-C16:0, iso-C16:0 3OH and iso-C17:0 3OH. Phosphatidylethanolamine was the major polar lipid. Strain WG47T was found to produce flexirubin-type pigments, while AS60T did not. These results, combined with phenotypic and biochemical data, suggest that strains AS60T and WG47T represent two novel species of Flavobacterium, for which the names Flavobacterium anseongense sp. nov. (AS60T=KACC 22413T=LMG 32491T) and Flavobacterium wongokense sp. nov. (WG47T=KACC 22407T=LMG 32500T) are proposed.

Lead (Pb2+) biosorption and bioaccumulation efficiency of Enterobacter chuandaensis DGI-2: Isotherm, kinetics and mechanistic study for bioremediation

Heavy metal (HM) contamination, particularly lead (Pb²⁺), threatens environmental and agricultural sustainability, necessitating effective remediation strategies. This study evaluates the Pb²⁺ sequestration potential of Enterobacter chuandaensis DGI-2, an HM-tolerant rhizobacterium isolated from a Pb-contaminated rhizosphere. DGI-2 exhibited high Pb²⁺ removal efficiency, achieving 94.73 % removal at 100 µg/mL and 69.09 % at 750 µg/mL over 96 h, primarily through cell surface and exopolysaccharide (EPS) adsorption. Biosorption studies demonstrated higher Pb²⁺ uptake in living biomass (102.95 mg/g, 68.63 %) than in dead biomass (98.61 mg/g, 65.74 %) under controlled conditions (0.5 g/L biomass, pH-6.5, 720 min). Mechanistic analyses revealed that Pb²⁺ adsorption primarily involved interactions with -OH, -COOH, and -PO₄³ ⁻ functional groups, facilitated by multilayer sorption, complexation, and ion exchange. Moreover, a 210.66 % increase in phosphatase activity promoted Pb²⁺ precipitation, forming stable Pb-phosphate minerals (e.g., Pb₅(PO₄)₃Cl, Pb₁₀(PO₄)₆(OH)₂), as confirmed by X-ray diffraction (XRD), significantly contributing to Pb sequestration. Regeneration studies demonstrated the biomass' reusability over four cycles. Soil microcosm experiments showed an 11.7-13.1 % reduction in bioavailable Pb, with greater stabilization in non-sterile soils, suggesting synergistic effects with native microbiota. Additionally, DGI-2 exhibited plant growth-promoting (PGP) traits, reducing phytotoxicity, enhancing soil health and phytostabilization potential, positioning it as a sustainable biosorbent for Pb²⁺ remediation.

Characterization of Streptomyces species with poly(3-hydroxybutyrate) degradation capabilities isolated from rice field soil

The shift towards sustainable alternatives to petroleum-based polymers has become essential for addressing environmental challenges. Among these alternatives, bio-plastics such as poly(3-hydroxybutyrate) (PHB) have gained considerable attention due to their biodegradability into water and carbon dioxide through microbial activity. PHB is one of the most widely commercialized bio-plastics. However, its excessive accumulation in the environment due to insufficient degradation remains a significant ecological concern. This study focused on isolating and characterizing PHB-degrading bacteria from soil samples collected from rice fields. Screening led to the identification of five PHB-degrading bacterial strains belonging to different genera. Among these, Streptomyces sp. AG7 and Streptomyces sp. RG41 were identified as the most effective PHB degraders. Their PHB-degrading abilities were evaluated in shake-flask cultures using PHB films as substrates. After 20 days of incubation at 37 °C, Streptomyces sp. AG7 and Streptomyces sp. RG41 achieved PHB degradation rates of approximately 74.7 % and 68.5 %, respectively. Additionally, both strains demonstrated the ability to produce indole-3-acetic acid (IAA), a key phytohormone that promotes plant growth, and exhibited phosphate-solubilizing activity, which enhances nutrient availability. Further analysis using scanning electron microscopy (SEM) revealed structural changes in the PHB films, while gel permeation chromatography (GPC) confirmed significant alterations in the polymer's molecular properties. These findings highlight the potential of utilizing soil-derived Streptomyces species for sustainable PHB waste management, in order to promote plant growth, improve soil fertility through phosphate solubilization, and contribute to agricultural sustainability.

Uliginosibacterium silvisoli sp. nov., Isolated from Subtropical Forest Soil in Hunan Province, China

A Gram negative bacterium, designated H3T, was isolated from a forest soil sample collected in Zhangjiajie National Forest Park, Hunan Province, PR China. Cells of strain H3T were yellow-pigmented, strictly aerobic, motile by means of a single polar flagellum. Growth occurred at 15-37 °C (optimum, 25-30 °C), pH 6.0-8.0 (optimum, 7.0) and 0-1.0% (w/v) NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequences and genome showed that strain H3T was affiliated to the genus Uliginosibacterium within the family Rhodocyclaceae of the class Betaproteobacteria and shared the highest sequence similarities with U. sediminicola M1-21 T (96.3%). The DNA G + C content of the genomic DNA was 61.4%. The major fatty acids of strain H3T were C16:0, summed feature 3 (16:1 ω7c/16:1 ω6c) and C12:0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipid, an unidentified aminolipid, three unidentified lipids, an unidentified glycolipid, and two uncharacterized phospholipids. The major respiratory quinone was ubiquinone-8. The dDDH and ANI values between strain H3T and the type strains of the genus Uliginosibacterium were 19.2-20.7% and 71.4-76.0%, respectively. Based on the evidences in this study, strain H3T represents a novel species of the genus Uliginosibacterium, for which the name Uliginosibacterium silvisoli sp. nov. is proposed. The type strain is H3T (= MCCC 1K09133T = KCTC 8564 T = JSACC 33374 T).

Comparative metabolomics reveals streptophenazines with anti-methicillin-resistant Staphylococcus aureus activity derived from Streptomyces albovinaceus strain WA10-1-8 isolated from Periplaneta americana

BACKGROUND

Streptophenazines, a class of phenazine compounds with a variety of alkyl side chains and activity against methicillin-resistant Staphylococcus aureus (MRSA), are mainly derived from soil or marine microbial secondary metabolites. However, the discovered phenazine compounds still do not meet the needs of the development of anti-MRSA lead compounds. Here, we examined secondary metabolites of Streptomyces albovinaceus WA10-1-8 isolated from Periplaneta americana, for streptophenazines with anti-MRSA activity.

RESULTS

In this study, a guidance method combining high-performance liquid chromatography-ultraviolet (HPLC-UV) with molecular networking analysis was used to isolate and identify a series of streptophenazines (A-T) from S. albovinaceus WA10-1-8. Among them, a new streptophenazine containing a dihydroxyalkyl chain structure named streptophenazine T was isolated and identified for the first time. The results of bioactivity assays showed that streptophenazine T had anti-MRSA activity with a minimum inhibitory concentration (MIC) of 150.23 µM, while the MICs of streptophenazine A, B, G, and F were 37.74-146.12 µM.

CONCLUSIONS

This study was the first to report multiple streptophenazine compounds with anti-MRSA activity expressed by Streptomyces isolated from insect niches. These results provided a valuable reference for future exploration of new streptophenazine compounds with activity against drug-resistant bacteria.

First Report and Pathogenicity Analysis of Photobacterium damselae subsp. piscicida in Cage-Cultured Black Rockfish (Sebastes schlegelii) Associated with Skin Ulcers

Photobacterium damselae subsp. Piscicida (PDP), a marine bacterium, has been reported to infect a variety of economically important marine species worldwide. Understanding the occurrence and pathogenicity of PDP is crucial for effective disease control and ensuring the success of aquaculture operations. In late August 2023, an epidemic outbreak of P. damselae subsp. piscicida DQ-SS1, accompanied by significant mortality, was recorded in cage-cultured black rockfish (Sebastes schlegelii) located on Daqin Island for the first time. Genomic analysis revealed that DQ-SS1 possesses 2 chromosomes, with a total size of 4,510,445 bp and 3923 predicted CDSs. Pathogenic genes analysis identified 573 and 314 genes related to pathogen-host interactions and virulence, respectively. Additionally, DQ-SS1 displayed susceptibility to 15 antimicrobials, was resistant to 11 antimicrobials, and was intermediately sensitive to four antibiotics. Meanwhile, the in vitro assay revealed that the extracellular products (ECP) of DQ-SS1 were lethal to macrophages and exhibited hemolysin, lipase, and amylase activities. Moreover, DQ-SS1 also demonstrated the ability to survive in fish serum and resist complement-mediated killing. The in vivo assay showed that the infected fish exhibited severe histopathological alterations, such as the infiltration of inflammatory cells, cellular degeneration and necrosis, and loose cell aggregation. Lastly, the in vivo infection assays revealed the LD50 of DQ-SS1 was 1.7 × 103 CFU/g. This is the first study to elucidate the pathogenicity and genomic characteristics of multidrug-resistant PDP in cage-cultured S. schlegelii, which contributes to the advancement of diagnostic and preventative strategies for this disease in marine-cultured fishes and provides information for an in-depth study of the pathogenic mechanism of PDP.

Mesorhizobium salmacidum sp. nov. and Mesorhizobium argentiipisi sp. nov. are symbionts of the dry-land forage legumes Lessertia diffusa and Calobota sericea

Legumes Lessertia diffusa and Calobota sericea, indigenous to South Africa, are commonly used as fodder crops with potential for sustainable livestock pasture production. Rhizobia were isolated from their root nodules grown in their respective soils from the Succulent Karoo biome (SKB) in South Africa, identified and characterized using a polyphasic approach. Sequence analysis of the 16S rRNA gene confirmed all isolates as Mesorhizobium members, which were categorized into two distinct lineages using five housekeeping protein-coding genes. Lineage I included 14 strains from both legumes, while Lineage II comprised a single isolate from C. sericea. Differences in phenotypic traits were observed between the lineages and corroborated by average nucleotide identity analyses. While all strains nodulated their original hosts, strains from C. sericea failed to effectively nodulate L. diffusa and vice versa. Phylogenetic analyses of nitrogen fixation (nifH) and nodulation (nodA, nodC) loci grouped all strains in a single clade, suggesting that unique symbiotic loci determine nodulation of these legumes. We designated Lineage I and II as Mesorhizobium salmacidum sp. nov. (Ld1326Ts; GCA_037179605.1Ts) and Mesorhizobium argentiipisi sp. nov. (Cs1330R2N1Ts; GCA_037179585.1Ts), using genome sequences as nomenclatural types according to the Nomenclatural Code for Prokaryotes using Sequence Data, thus avoiding complications with South Africa's biodiversity regulations. Identifying effective microsymbionts of L. diffusa and C. sericea is essential for conservation of Succulent Karoo Biome, where indigenous invasive species like Vachellia karroo and non-native Australian acacia species are present. Furthermore, targeted management practices using effective symbionts of the studied legumes can sustain the biome's socio-economic contribution through fodder provision.

Leaf Beetle Symbiotic Bacteria Degrade Chlorogenic Acid of Poplar Induced by Egg Deposition to Enhance Larval Survival

Insect symbiotic microbiota acting as a third-party force of plant-insect interactions, play a significant role in insect hosts tolerance to phytochemical defences. However, it remains unknown whether insect symbiotic bacteria can assist the host in degrading phytochemical defences induced by egg deposition. Plagiodera versicolora is a worldwide forest pest. Our study showed that P. versicolora egg deposition on Populus davidiana × Populus bolleana induced significant changes in the transcriptome and metabolome of leaves. Combined qRT-PCR and LC-MS quantitative analysis of metabolic pathways showed that the contents of chlorogenic acid and rutin were significantly increased upon egg deposition in poplar. Bioassays indicated that the high concentration of chlorogenic acid induced by egg deposition could significantly reduce the performance of germ-free larvae. Six symbiotic bacterial strains with potential ability to degrade chlorogenic acid were isolated and identified. Their degradation products did not affect larval survival either. In vivo inoculation assays showed that four of those symbiotic bacteria could assist in the degradation of high concentration of chlorogenic acid induced by egg deposition and improve the larval survival. Our study provides clear evidence that the insect symbiotic bacteria can mediate the tolerance of herbivorous insects against plant toxins induced by egg deposition.

Erwinia aeris sp. nov., A Novel Bacterium Isolated from the Surface of an Ore in Hubei Province, China

A novel Gram-stain-negative, phosphate-solubilizing and siderophore producing bacterium, which we designated as strain ACCC 02193T, was separated from ore, collected in Zhongxiang, Hubei of China. Phylogenetic analysis based on 16S rRNA gene sequences showed strain ACCC 02193T is in the genus Erwinia and had highest similarities to Erwinia tasmaniensis DSM 17950T (99.32%) and Erwinia billingiae DSM 17872T (98.77%). However, phylogenomic analyses clearly showed that the strain ACCC 02193T was most closely related to Erwinia phyllosphaerae CMYE1T. The strain grew at 28 °C-30 °C optimally, with 0-6% (w/v) NaCl (optimum 5%), and in the range of pH 4.0-10.0 (optimum pH 8.0). Menaquinone was identified as Q-8. The predominant fatty acids (> 10.0%) were C16:0, C17:0 cyclo, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). Genome comparisons showed that the strain shared ≤ 82.8% average nucleotide identity (ANI) and ≤ 27.2% in silico DNA-DNA hybridization (DDH) values with closely related type strains, respectively, which supported our conclusion that ACCC 02193T represented a novel species in the genus Erwinia. The DNA G+C content of the strain was 55.7%. Based on the results of physiological and biochemical characteristics, genotypic data, as well as genome comparisons, we demonstrated that type strain ACCC 02193T (= GDMCC 1.4563T = JCM 37069T) is a novel species in the genus Erwinia, and we propose the name Erwinia aeris sp. nov.

Marine Flavobacteriaceae produce zeaxanthin via the mevalonate pathway

Zeaxanthin, an oxygenated carotenoid derivative with potent antioxidative properties, is produced by many organism taxa. Flavobacteriaceae are widely distributed in marine environments; however, the zeaxanthin biosynthesis property in this family remains incompletely explored. Here, we characterized zeaxanthin production by marine Flavobacteriaceae strains and elucidated underlying molecular mechanisms. Eight Flavobacteriaceae strains were isolated from the phycosphere of various dinoflagellates. Analyses of the zeaxanthin production in these strains revealed yields ranging from 5 to 3289 µg/g of dry cell weight. Genomic and molecular biology analyses revealed the biosynthesized zeaxanthin through the mevalonate (MVA) pathway diverging from the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway commonly observed in most Gram-negative bacteria. Furthermore, comprehensive genome analyses of 322 culturable marine Flavobacteriale strains indicated that the majority of Flavobacteriaceae members possess the potential to synthesize zeaxanthin using precursors derived from the MVA pathway. These data provide insight into the zeaxanthin biosynthesis property in marine Flavobacteriaceae strains, highlighting their ecological and biotechnological relevance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00268-4.

Vogesella oryzagri sp. nov., isolated from the rhizosphere of rice and in silico genome mining for the prediction of biosynthetic gene clusters

A Gram-stain-negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-64T, was isolated from the rhizosphere of rice. The colonies were observed to be creamy white-coloured, smooth, spherical and 0.5-1.1 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAHUQ-64T was able to grow at 10-40 °C, at pH 5.0-9.5 and in the presence of 0-2.0% NaCl (w/v). The strain was positive for both catalase and oxidase tests. The strain was positive for hydrolysis of l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Vogesella and is closely related to Vogesella oryzae L3B39T (98.6% sequence similarity) and Vogesella facilis TTM-24T (98.2%). The novel strain MAHUQ-64T has a draft genome size of 3 827 146 bp (22 contigs), annotated with 3612 protein-coding genes, 74 tRNA and 4 rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-64T and its closest member V. oryzae L3B39T were 86.5 and 33.4%, respectively. In silico genome mining revealed several biosynthetic gene clusters in the genome of the novel strain MAHUQ-64T. The genomic DNA G+C content was determined to be 63.4 mol%. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as summed feature 3 (comprising C16  :  1 ω7c and/or C16  :  1 ω6c) and C16  :  0. Based on dDDH, ANI value, genotypic analysis and chemotaxonomic and physiological data, strain MAHUQ-64T represents a novel species within the genus Vogesella, for which the name Vogesella oryzagri sp. nov. is proposed, with MAHUQ-64T (=KACC 22245T=CGMCC 1.19000T) as the type strain.

Paenibacillus mesotrionivorans sp. nov., a Mesotrione-Degrading Strain Isolated from Soil

A Gram-stain-positive, facultatively anaerobic, motile with peritrichous flagella, and rod-shaped bacterium, designated as P15T, was isolated from an agricultural soil sample collected in Jiangxi Province, PR China. Strain P15T completely degraded 100 mg/L of mesotrione, a herbicide, within 48 h of incubation. Strain P15T grew at 15-42 °C (optimum 30 °C), pH 6.0-9.0 (optimum 7.0), and 0-4.0% (w/v) NaCl (optimum 1.0%). Strain P15T exhibited less than 93.3% 16S rRNA gene sequence similarity with type strains of genus Paenibacillus. In the phylogenetic tree based on 16S rRNA gene sequences, strain P15T was clustered in genus Paenibacillus and formed a subclade with P. cavernae C4-5T, P. contaminans CKOBP-6T, and P. doosanensis CAU 1005T. The major cellular fatty acids (≥ 5% of the total) were anteiso-C15:0, iso-C16:0, C14:0, C16:0, and iso-C14:0. The predominant respiratory quinone was MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycero, phosphatidylethanolamine, one unidentified glycolipid, one unidentified aminophosphoglycolipid, two unidentified aminophospholipids, two unidentified phospholipid, and two unidentified lipids. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The DNA G + C content was 53.9 mol%. Based on the phylogenetic, phenotypic, and chemotaxonomic characteristics, strain P15T represents a novel species within genus Paenibacillus, for which the name Paenibacillus mesotrionivorans sp. nov is proposed, with strain P15T (= MCCC 1K09191T = KCTC 43705T) as the type strain.

Lentilactobacillus terminaliae sp. nov., isolated from tree bark (Terminalia ivorensis Chev.) and its antioxidant activity

A Gram-stain-positive, facultatively anaerobic, rod-shaped strain, designated SPB1-3T, was isolated from tree bark. This strain exhibited heterofermentative production of dl-lactic acid from glucose. Optimal growth was observed at 25-40 °C, pH 4.0-7.0, and in the presence of 3% (w/v) NaCl. The cell wall peptidoglycan contained lysine and aspartic acid. The predominant fatty acids identified were C16:0 and the Summed feature 7 (C19 :1  ω7c/C19:1  ω6c and/or C19:1  ω6c/ω7c/19cy). The polar lipid profile included phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol, along with two unidentified phospholipids, two unidentified amino lipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain SPB1-3T within the genus Lentilactobacillus, showing a close relation to Lentilactobacillus kosonis NBRC 111893T (99.86%) and Lentilactobacillus curieae CCTCC M 2011381T (98.65%). The whole genome of strain SPB1-3T comprised 1 932 998 base pairs with 1955 coding genes and a DNA G+C content of 37.8%. Digital DNA-DNA hybridization between strain SPB1-3T and closely related type strains ranged from 19.50 to 27.20%. The average nucleotide identity ranged from 84.21 to 85.56%, and the average amino acid identity ranged from 57.25 to 85.99%, both falling below the established thresholds for species delineation. Strain SPB1-3T was clearly distinguishable from related Lentilactobacillus species based on its phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence similarity and whole genome analysis. Additionally, the strain exhibited radical scavenging activity at 66.92% and demonstrated 82.32% inhibition in the tyrosinase inhibitory assay. These findings support the classification of strain SPB1-3T as a novel species within the genus Lentilactobacillus, for which the name Lentilactobacillus terminaliae sp. nov. is proposed. The type strain is SPB1-3T (=JCM 35081T=TISTR 10005T).

Paenibacillus zeirhizosphaerae sp. nov., isolated from surface of the maize (Zea mays) roots in a horticulture field, Hungary

A novel Gram-stain-positive, rod-shaped, endospore-forming bacterium with peritrichous flagella, designated as P96T was isolated from the surface of maize roots. Strain P96T grew optimally at 28 °C, pH 7.0. The strain contained A1γ meso-Dpm-direct in the cell-wall peptidoglycan. The dominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The genome size of strain P96T was 4.8 Mb, and the G+C content was 50.01%. Phylogenomic analyses based on the whole-genome sequences classified the strain into the genus Paenibacillus. The digital DNA-DNA hybridization and average nucleotide identity relatedness analysis resulted in values below the threshold for prokaryotic species delineation, with the highest values observed for Paenibacillus enshidis KCTC 33519T (29.4 and 85.2%, respectively). Genotypic data together with phenotypic properties supported the classification of strain P96T as representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus zeirhizosphaerae sp. nov. is proposed. The type strain is P96T (=LMG 32802T = NCAIM B 02678T).

Testacosides A-D, glycoglycerolipids produced by Microbacterium testaceum isolated from Tedania brasiliensis

Marine bacteria living in association with marine sponges have proven to be a reliable source of biologically active secondary metabolites. However, no studies have yet reported natural products from Microbacterium testaceum spp. We herein report the isolation of a M. testaceum strain from the sponge Tedania brasiliensis. Molecular networking analysis of bioactive pre-fractionated extracts from culture media of M. testaceum enabled the discovery of testacosides A-D. Analysis of spectroscopic data and chemical derivatizations allowed the identification of testacosides A-D as glycoglycerolipids bearing a 1-[α-glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol moiety connected to 12-methyltetradecanoic acid for testacoside A (1), 14-methylpentadecanoic acid for testacoside B (2), and 14-methylhexadecanoic acid for testacosides C (3) and D (4). The absolute configuration of the monosaccharide residues was determined by 1H-NMR analysis of the respective diastereomeric thiazolidine derivatives. This is the first report of natural products isolated from cultures of M. testaceum. KEY POINTS: • The first report of metabolites produced by Microbacterium testaceum. • 1-[α-Glucopyranosyl-(1 → 3)-(α-mannopyranosyl)]-glycerol lipids isolated and identified. • Microbacterium testaceum strain isolated from the sponge Tedania brasiliensis.

Antibacterial activity and biosynthetic potential of Streptomyces sp. PBR19, isolated from forest rhizosphere soil of Assam

An Actinomycetia isolate, designated as PBR19, was derived from the rhizosphere soil of Pobitora Wildlife Sanctuary (PWS), Assam, India. The isolate, identified as Streptomyces sp., shares a sequence similarity of 93.96% with its nearest type strain, Streptomyces atrovirens. This finding indicates the potential classification of PBR19 as a new taxon within the Actinomycetota phylum. PBR19 displayed notable antibacterial action against some ESKAPE pathogens. The ethyl acetate extract of PBR19 (EtAc-PBR19) showed the lowest minimum inhibitory concentration (MIC) of ≥ 0.195 µg/mL against Acinetobacter baumannii ATCC BAA-1705. A lower MIC indicates higher potency against the tested pathogen. Scanning electron microscope (SEM) findings revealed significant changes in the cytoplasmic membrane structure of the pathogen. This suggests that the antibacterial activity may be linked to the disruption of the microbial membrane. The predominant chemical compound detected in the EtAc-PBR19 was identified as phenol, 3,5-bis(1,1-dimethylethyl), comprising 48.59% of the area percentage. Additionally, PBR19 was found to contain the type II polyketide synthases (PKS type II) gene associated with antibiotic synthesis. The predicted gene product of PKSII was identified as the macrolide antibiotic Megalomicin A. The taxonomic distinctiveness, potent antibacterial effects, and the presence of a gene associated with antibiotic synthesis suggest that PBR19 could be a valuable candidate for further exploration in drug development and synthetic biology. The study contributes to the broader understanding of microbial diversity and the potential for discovering bioactive compounds in less-explored environments.

Expanding the Stenotrophomonas maltophilia complex: phylogenomic insights, proposal of Stenotrophomonas forensis sp. nov. and reclassification of two Pseudomonas species

A novel Stenotrophomonas species was isolated as a contaminant in viral transport media at the District of Columbia Department of Forensic Sciences Public Health Laboratory. Phylogenomic and biochemical analyses of the isolate determined that it represented a novel species within Stenotrophomonas. Related strains in public genome databases suggested that this novel species is associated with clinically acquired infections, similar to closely related Stenotrophomonas maltophilia. The name Stenotrophomonas forensis sp. nov. is proposed. Comparative genomic and phylogenetic analyses of the S. maltophilia complex reveal that Stenotrophomonas africana is an independent species and is not a later heterotypic synonym of S. maltophilia. We also propose the transfer of two misclassified Pseudomonas species into Stenotrophomonas as Stenotrophomonas beteli comb. nov. and Stenotrophomonas hibiscicola comb. nov. The type strain for S. forensis sp. nov. is DFS-20110405T (=ATCC TSD-272T=NCTC 14893T).

Diversity, antibacterial and phytotoxic activities of actinomycetes associated with Periplaneta fuliginosa

Background

Insect-associated actinomycetes represent a potentially rich source for discovering bioactive metabolites. However, the diversity, antibacterial and phytotoxic activities of symbiotic actinomycetes associated with Periplaneta fuliginosa have not yet been conducted.

Results

A total of 86 strains of actinomycetes were isolated from the cornicles and intestines of both nymphs and adults of P. fuliginosa. Diversity analysis revealed that the isolated strains were preliminarily identified as 17 species from two genera, and the dominant genus was Streptomyces. A total of 36 crude extracts (60%) obtained from the supernatant of the 60 fermented strains exhibited a potent antibacterial activity against at least one tested pathogenic bacterium. Among these active strains, 27 crude extracts (75%) exhibited phytotoxic activity against the radicle of Echinochloa crusgalli. Furthermore, seven known compounds, including methoxynicotine (1), (3Z,6Z)-3-(4-methoxybenzylidene)-6-(2-methylpropyl) piperazine-2,5-dione (2), XR334 (3), 1-hydroxy-4-methoxy-2-naphthoic acid (4), nocapyrone A (5), β-daucosterol (6), and β-sitosterol (7) were isolated from an active rare actinomycete Nocardiopsis sp. ZLC-87 which was isolated from the gut of adult P. fuliginosa. Among them, compound 4 exhibited moderate antibacterial activity against Micrococcus tetragenus, Staphylococcus aureus, Escherichia coli, and Pseudomonas syringae pv. actinidiae with the zone of inhibition (ZOI) of 14.5, 12.0, 12.5, and 13.0 mm at a concentration of 30 μg/disc, respectively, which was weaker than those of gentamicin sulfate (ZOI of 29.5, 19.0, 18.5, and 24.5 mm). In addition, the compound 4 had potent phytotoxic activity against the radicle of E. crusgalli and Abutilon theophrasti with the inhibition rate of 65.25% and 92.68% at the concentration of 100 μg/mL.

Conclusion

Based on these findings, this study showed that P. fuliginosa-associated actinomycetes held promise for the development of new antibiotic and herbicide resources.

Protective effects of Marinobacter nauticus strain GH3 exopolysaccharide on the Oreochromis niloticus model for Alzheimer's disease

Marinobacter nauticus strain GH3 was isolated from the Red Sea, Sharm Elshiekh, and classified according to cultural attributes, biochemical properties, and the analysis of genetic relationships using 16 S rRNA sequences. A substantial proportion of exopolysaccharides (EPS) in GH3-EPS contained a sulfate content of 25.4%, uronic acid (12.18%), and N-acetylglucosamine (13.6%). The composition of monosaccharides in this fraction consists of glucose, glucoronic acid, arabinose, and xylose by 2:4:3:3, respectively. SEM showed a flower-like shape with white bundles on the GH3-EPS surface. GH3-EPS enhancement of the RAW264.7 macrophage line RAW 264.7 ATTC number J774 cell proliferation via MTT assay for cell viability. GH3-EPS had a high stimulation effect on releasing TNF-alpha and IL-10. Followed by its effect against cyclooxygenase (COX-2) and lipoxygenase (LOX), with IC50s of 14.74 and 19.4 µg/ml, respectively. Antioxidant activity was evaluated for GPx-4, GSS, and MDA with highly significant results, and for DPPH, ABTS, and iron chelating with IC50 (43.51, 31.27, and 84.96 µg/ml, respectively). AChE was inhibited by a mean of 52.92 ± 4.54 and 68.22 ± 5.64 µg/ml. In a fish animal model, GH3-EPS demonstrated a positive treatment effect for AD, supporting biochemical studies, histopathology for some brain parts, and toxicity.

Two Novel Bacterial Species, Rhodanobacter lycopersici sp. nov. and Rhodanobacter geophilus sp. nov., Isolated from the Rhizosphere of Solanum lycopersicum with Plant Growth-Promoting Traits

Two novel bacterial species were isolated from the rhizosphere of Solanum lycopersicum (tomato plant), both exhibiting plant growth-promoting properties. Two isolated strains, Rhodanobacter lycopersici sp. nov. Si-cT and Rhodanobacter geophilus sp. nov. S2-gT, were classified through a polyphasic approach, confirming their novel status within the Rhodanobacter genus. The strains demonstrated a remarkable tolerance to extreme pH conditions, with R. lycopersici Si-cT surviving in pH 3.0-13.0 and R. geophilus S2-gT tolerating pH 2.0-13.0. Additionally, both strains exhibited multiple plant growth-promoting traits, including indole-3-acetic acid and ammonia production, phosphate solubilization, and siderophore formation. These characteristics suggest that the two strains may play an important role in promoting plant growth, especially in soils with variable pH levels. However, since the direct impact on plant growth was not experimentally tested, the potential of these bacteria for agricultural applications remains to be confirmed through further research. This study expands our understanding of the diversity within the Rhodanobacter genus and provides insights into the potential use of these novel species in sustainable agriculture.

Isolation of Massilia species capable of degrading Poly(3-hydroxybutyrate) isolated from eggplant (Solanum melongena L.) field

Poly(3-hydroxybutyrate) (PHB) is crucial for replacing petroleum-based plastics, an essential step towards fostering a bio-based economy. This shift is urgently needed to safeguard human health and preserve natural ecosystems. PHB is one of the most extremely commercialized bio-plastics. Although. significant progress has been made in identifying bacteria that produce PHB, fewer bacteria capable of degrading it have been discovered. Four newly isolated Massilia strains capable of degrading PHB were discovered in eggplant (Solanum melongena L.) field soil. Their PHB-degrading abilities were investigated under different temperatures and media using emulsified solid-media based cultures. The strains belong to the genus Massilia, were evaluated for their effectiveness. Among them, Massilia sp. JJY02, was selected for its exceptional PHB degradation. PHB degradation was confirmed by monitoring changes in the physical and chemical properties of PHB films using scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR) and gel permeation chromatography (GPC). After 20 days of cultivation with PHB film, Massilia sp. JJY02 achieved approximately 90% PHB degradation at 28 °C. All the novel strains were capable of producing carotenoid-type pigments and indole-acetic acid (IAA). Among them, Massilia sp. JJY03 and JJY04 showed phosphate solubilization activity. This study demonstrated that soil bacteria from eggplant have both PHB-degrading and plant growth promoting capabilities, marking the first instance of showing that species of Massilia can degrade PHB.

Unveiling the role of emerging metagenomics for the examination of hypersaline environments

Hypersaline ecosystems are distributed all over the globe. They are subjected to poly-extreme stresses and are inhabited by halophilic microorganisms possessing multiple adaptations. The halophiles have many biotechnological applications such as nutrient supplements, antioxidant synthesis, salt tolerant enzyme production, osmolyte synthesis, biofuel production, electricity generation etc. However, halophiles are still underexplored in terms of complex ecological interactions and functions as compared to other niches. The advent of metagenomics and the recent advancement of next-generation sequencing tools have made it feasible to investigate the microflora of an ecosystem, its interactions and functions. Both target gene and shotgun metagenomic approaches are commonly employed for the taxonomic, phylogenetic, and functional analyses of the hypersaline microbial communities. This review discusses different types of hypersaline niches, their residential microflora, and an overview of the metagenomic approaches used to investigate them. Various applications, hurdles and the recent advancements in metagenomic approaches have also been focused on here for their better understanding and utilization in the study of hypersaline microbiome.

Sporosarcina hypophthalmichthys sp. nov. Isolated From Gastrointestinal Tract of Fish Hypophthalmichthys molitrix (Valenciennes, 1844)

A rod-shaped, motile, Gram-stain-positive bacterial strain RKN2T, was isolated from gut of silver carp (Hypophthalmichthys molitrix) residing in Gobindsagar reservoir, Himachal Pradesh, India. Having the greatest sequence similarity to Sporosarcina koreensis F73T (98.51%), Sporosarcina luteola Y1T (98.4%) and Sporosarcina aquimarina SW28T (98.36%), the 16S rRNA gene phylogeny confirmed the belonging of strain RKN2T to genus Sporosarcina. Digital DNA-DNA hybridization values were 21.7%, 20.6%, and 19.2%, and average nucleotide identity values were 76.42%, 80.16%, 76.51%, of strain RKN2T with Sporosarcina koreensis F73T, Sporosarcina luteola Y1T, and Sporosarcina aquimarina SW28T, respectively. The genomic analysis of strain RKN2T showed various biological properties including nitrate reduction, genes responsible for carbohydrate-active enzymes production, antimicrobial compounds, as well as potential metabolism of aromatic compounds and heavy metals. G+C composition of RKN2T genome was 52.7%. This strain can grow in temperatures between 10°C and 40°C (optimum, 28°C-30°C), NaCl concentrations up to 6.0% (w/v), and 6.0-8.0 (optimum, 6.5-7.5) pH range. MK-7 was the dominant respiratory quinone, A-4 type cell wall peptidoglycan was present with anteiso-C15:0, iso-C15: 0, and anteiso-C17:0 being the major fatty acids and Lys-Glu being main amino acids. Diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine were the strain RKN2T's three main polar lipids. The strain is a novel species under genus Sporosarcina based on polyphasic approach and the name Sporosarcina hypophthalmichthys sp. nov. is given for strain RKN2T. RKN2T is a type strain (= MCC 4365T = JCM34522T = CCM9112T).

Diversity and Bioactivity of Endophytic Actinobacteria Associated with the Roots of Artemisia herba-alba Asso from Algeria

The isolation of endophytic actinobacteria from the roots of wild populations of Artemisia herba-alba Asso, a medicinal plant collected from the arid lands of Algeria, is reported for the first time. Forty-five actinobacterial isolates were identified by molecular analysis and in vitro evaluated for antimicrobial activity and plant growth-promoting (PGP) abilities (1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, nitrogen fixation, phosphate and potassium solubilization, ammonia, and siderophores production). The phylogenetic relationships based on 16S rRNA gene sequences show that the genus Nocardioides (n = 23) was dominant in the sampled localities. The remaining actinobacterial isolates were identified as Promicromonospora (n = 11), Streptomyces (n = 6), Micromonopora (n = 3), and Saccharothrix (n = 2). Only six (13.33%) strains (five Streptomyces and one Saccharothrix species) were antagonistic in vitro against at least one or more indicator microorganisms. The antimicrobial activity of actinobacterial strains targeted mainly Gram-positive bacteria. The results demonstrate that more than 73% of the isolated strains had ACC deaminase activity, could fix atmospheric nitrogen and were producers of ammonia and siderophores. However, only one (2.22%) strain named Saccharothrix sp. BT79 could solubilize phosphorus and potassium. Overall, many strains exhibited a broad spectrum of PGP abilities. Thus, A. herba-alba provides a source of endophytic actinobacteria that should be explored for their potential biological activities.

Garlic Bioconverted by Bacillus subtilis Stimulates the Intestinal Immune System and Modulates Gut Microbiota Composition

SCOPE

This study evaluates the potential of bioconverted garlic ferments (BGFs) to stimulate the intestinal immune system and modulate cecal microbiota composition.

METHODS AND RESULTS

In vitro, BGF significantly enhances Peyer's patch (PP)-mediated bone marrow cell proliferation and increases the production of interferon-gamma (IFN-γ), granulocyte macrophage-colony stimulating factor (GM-CSF), interleukin (IL)-6, and immunoglobulin A (IgA) but not IL-4, IL-5, and immunoglobulin E (IgE). Oral administration of BGF to C3H/HeN mice for 4 weeks significantly increases the GM-CSF (42.1-45.8 pg mL-1) and IFN-γ (6.5-12.1 pg mL-1) levels in PP cells. BGF also significantly elevates the levels of tumor necrosis factor-alpha (TNF-α, 165.0-236.3 pg mg-1), GM-CSF (2.4-3.0 ng mg-1), and IFN-γ (1.5-3.2 ng mg-1) in the small intestinal fluid, and TNF-α (2.2-3.1 pg mL-1) and IFN-γ (10.3-0.21.5 pg mL-1) in the mouse serum. Cecal microbial analysis reveals that BGF increases Bacteroidota and Verrucomicrobiota and decreases Actinobacteria and Bacillota at the phylum level in mice. At the genus level, BGF significantly increases the abundance of Fusimonas (250 mg kg-1 BW-1 day-1), Bacteroides (125 and 250 mg kg-1 BW-1 day-1), and Akkermansia (125 mg kg-1 BW-1 day-1) and decreases that of Bifidobacterium (62.5 and 250 mg kg-1 BW-1 day-1) and Limosilactobacillus (125 and 250 mg kg-1 BW-1 day-1).

CONCLUSION

This study provides the first evidence of BGF's ability to modulate the intestinal immune system and gut microbiota, supporting its potential as a novel functional material to enhance gut immunity.

Variation and functional profile of gut bacteria in the scarab beetle, Anomala dimidiata, under a cellulose-enriched microenvironment

This study utilized cultivable methods and 16 S amplicon sequencing to compare taxonomic profiles and functional potential of gut bacteria in the scarab beetle, Anomola dimidiata, under cellulose-enriched conditions. Eight culturable cellulolytic gut bacteria were isolated from the midgut and hindgut of the scarab larvae, respectively. 16 S amplicon sequencing evinced that the most represented taxonomic profiles at phylum level in the fermentation chamber and midgut were Bacillota (71.62 and 56.76%), Pseudomonadota (22.66 and 36.89%) and Bacteroidota (2.7 and 2.81%). Bacillota (56.74 and 91.39%) were significantly enriched in the midgut with the addition of cellulose. In contrast, Bacillota and Psedomonadota were significantly enriched in the fermentation chamber. Carbohydrate metabolism was up-regulated in the midgut, while nitrogen and phosphorus metabolism were up-regulated in the fermentation chamber, suggesting these symbionts' possible metabolic roles to the host. An analysis of total cellulases as well as amplicon sequence variants indicated that the gut bacteria belonging to Acinetobacter, Bacillus, Brucella, Brevibacillus, Enterobacter, Lysinibacillus and Paenibacillus are involved in nutrition provisioning. These results have provided additional insights into the gut bacteria associated with cellulose digestion in A. dimidiata and created a platform for bioprospecting novel isolates to produce biomolecules for biotechnological use, besides identifying eco-friendly targets for its management.

Diversity and Activity of Bacteria Cultured from a Cup-The Sponge Calyx nicaeensis

Marine sponges are well-known for hosting rich microbial communities. Sponges are the most prolific source of marine bioactive compounds, which are frequently synthesized by their associated microbiota. Calyx nicaeensis is an endemic Mediterranean sponge with scarce information regarding its (bioactive) secondary metabolites. East Mediterranean specimens of mesophotic C. nicaeensis have never been studied. Moreover, no research has inspected its associated bacteria. Thus, we studied the sponge's bacterial diversity and examined bacterial interspecific interactions in search of a promising antibacterial candidate. Such novel antimicrobial agents are needed since extensive antibiotic use leads to bacterial drug resistance. Bacteria cultivation yielded 90 operational taxonomic units (OTUs). A competition assay enabled the testing of interspecific interactions between the cultured OTUs. The highest-ranked antagonistic bacterium, identified as Paenisporosarcina indica (previously never found in marine or cold habitats), was mass cultured, extracted, and separated using size exclusion and reversed-phase chromatographic methods, guided by antibacterial activity. A pure compound was isolated and identified as 3-oxy-anteiso-C15-fatty acid-lichenysin. Five additional active compounds await final cleaning; however, they are lichenysins and surfactins. These are the first antibacterial compounds identified from either the C. nicaeensis sponge or P. indica bacterium. It also revealed that the genus Bacillus is not an exclusive producer of lichenysin and surfactin.

Phylogenomic Analysis Supports the Reclassification of Caldicoprobacter faecalis (Winter et al. 1988) Bouanane-Darenfed et al. (2015) as a Later Heterotypic Synonym of Caldicoprobacter oshimai Yokoyama et al. (2010)

This study employs genome-based methodologies to explore the taxonomic relationship between Caldicoprobacter faecalis DSM 20678T and Caldicoprobacter oshimai DSM 21659T. The genome-based similarity indices calculations consisting of digital DNA-DNA Hybridization (dDDH), Average Amino Aid Identity (AAI), and Average Nucleotide Identity (ANI) between the genomes of these two type strains yielded percentages of 91.2%, 98.9%, and 99.1%, respectively. These values were above the recommended thresholds of 70% (dDDH) and 95-96% (ANI and AAI) for bacterial species delineation, indicating a shared taxonomic position for C. faecalis and C. oshimai. Furthermore, analysis utilizing the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and constructing a Maximum Likelihood core-genes tree using FastTree2 consistently demonstrated the close relationship between C. faecalis DSM 20678T and C. oshimai DSM 21659T, evident from their clustering in the core-genes phylogenomic tree. Based on these comprehensive findings, we propose the reclassification of C. faecalis as a later heterotypic synonym of C. oshimai.

Analysis of genomic and characterization features of Luteolibacter soli sp. nov., isolated from soil

The strain designated as Y139T is a novel Gram-stain-negative, aerobic, and non-motile bacterium, was isolated from a soil sample in McClain County, Oklahoma, United States. The cells of strain Y139T were a rod-shaped, with the width of 0.4-0.7 μm and the length of 1.5-2.0 μm . Growth occurred at 20-37°C (optimum, 30°C), pH 5.5-9.5 (optimum, pH 7.0), and 0-1.0% NaCl (w/v) (optimum, 0%). The polar lipid profiles included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, and an unidentified lipid. The major fatty acids included C16:0, iso-C14:0, and C16:1 ω9c. Menaquinone-9 (MK-9) was recognized as the only respiratory quinone. Strain Y139T showed the highest 16S rRNA gene sequence similarity to Luteolibacter flavescens MCCC 1K03193T (98.3%). Phylogenetic analysis positioned it within the genus Luteolibacter. The draft genome of strain Y139T consisted of 7,106,054 bp, and contained 5,715 open reading frames (ORFs), including 5,656 coding sequences (CDSs) and 59 RNA genes. The genomic DNA G + C content was found to be 62.5%. Comparing strain Y139T with L. flavescens MCCC 1K03193T and Luteolibacter arcticus CCTCC AB 2014275T, the average nucleotide identity (ANI) values were 80.6 and 82.1%, respectively. Following phylogenetic, physiological, biochemical, and chemotaxonomic analyses, a novel species within the genus Luteolibacter, designated as Luteolibacter soli sp. nov., was proposed for strain Y139T, which was also assigned as the type strain (=KCTC 92644T = MCCC 1H01451T). Further analysis of core genes across 9 Luteolibacter species uncovered significant genomic divergence, particularly in those related to cofactor, vitamin, and energy metabolism. Analysis of biogeographic distribution suggested that lake and soil were the main habitats for the genus Luteolibacter. Additionally, the genus Luteolibacter was sensitive to climate warming and precipitation.

The Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications

This study aims to evaluate the in silico genomic characteristics of five species of the genus Planotetraspora: P. kaengkrachanensis, P. mira, P. phitsanulokensis, P. silvatica, and P. thailandica, with a view to their application in therapeutic research. The 16S rRNA comparison indicated that these species were phylogenetically distinct. Pairwise comparisons of digital DNA-DNA hybridization (dDDH) and OrthoANI values between these studied type strains indicated that dDDH values were below 62.5%, while OrthoANI values were lower than 95.3%, suggesting that the five species represent distinct genomospecies. These results were consistent with the phylogenomic study based on core genes and the pangenome analysis of these five species within the genus Planotetraspora. However, the genome annotation showed some differences between these species, such as variations in the number of subsystem category distributions across whole genomes (ranging between 1979 and 2024). Additionally, the number of CAZYme (Carbohydrate-Active enZYme) genes ranged between 298 and 325, highlighting the potential of these bacteria for therapeutic research applications. The in silico physico-chemical characteristics of cellulases from Planotetraspora species were analyzed. Their 3D structure was modeled, refined, and validated. A molecular docking analysis of this cellulase protein structural model was conducted with cellobiose, cellotetraose, laminaribiose, carboxymethyl cellulose, glucose, and xylose ligand. Our study revealed significant interaction between the Planotetraspora cellulase and cellotetraose substrate, evidenced by stable binding energies. This suggests that this bacterial enzyme holds great potential for utilizing cellotetraose as a substrate in various applications. This study enriches our understanding of the potential applications of Planotetraspora species in therapeutic research.

Physiological Basis of Plant Growth Promotion in Rice by Rhizosphere and Endosphere Associated Streptomyces Isolates from India

This study demonstrated the plant growth-promoting capabilities of native actinobacterial strains obtained from different regions of the rice plant, including the rhizosphere (FT1, FTSA2, FB2, and FH7) and endosphere (EB6). We delved into the molecular mechanisms underlying the beneficial effects of these plant-microbe interactions by conducting a transcriptional analysis of a select group of key genes involved in phytohormone pathways. Through in vitro screening for various plant growth-promoting (PGP) traits, all tested isolates exhibited positive traits for indole-3-acetic acid synthesis and siderophore production, with FT1 being the sole producer of hydrogen cyanide (HCN). All isolates were identified as members of the Streptomyces genus through 16S rRNA amplification. In pot culture experiments, rice seeds inoculated with strains FB2 and FTSA2 exhibited significant increases in shoot dry mass by 7% and 34%, respectively, and total biomass by 8% and 30%, respectively. All strains led to increased leaf nitrogen levels, with FTSA2 demonstrating the highest increase (4.3%). On the contrary, strains FB2 and FT1 increased root length, root weight ratio, root volume, and root surface area, leading to higher root nitrogen content. All isolates, except for FB2, enhanced total chlorophyll and carotenoid levels. Additionally, qRT-PCR analysis supported these findings, revealing differential gene expression in auxin (OsAUX1, OsIAA1, OsYUCCA1, OsYUCCA3), gibberellin (OsGID1, OsGA20ox-1), and cytokinin (OsIPT3, OsIPT5) pathways in response to specific actinobacterial treatments. These actinobacterial strains, which enhance both aboveground and belowground crop characteristics, warrant further evaluation in field trials, either as individual strains or in consortia. This could lead to the development of commercial bioinoculants for use in integrated nutrient management practices.

Pseudohoeflea coraliihabitans sp. nov., a poly-β-hydroxybutyrate-producing, halotolerant bacterium isolated from coral sediment in the Dapeng peninsula (Guangdong, China)

A Gram-stain-negative, strictly aerobic, motile, flagellated, rod-shaped, halotolerant, and poly-β-hydroxyalkanoate-producing bacterium, designated DP4N28-3T, was isolated from offshore sediment surrounding hard coral in the Dapeng peninsula (Guangdong, PR China). Growth occurred at 15-35 °C (optimal at 30 °C), pH 6.0-9.5 (optimal at 6.0-7.0), and 0.0-30.0 % NaCl concentration (w/v, optimal at 0.0-2.0 %), showing halotolerance. Phylogeny based on 16S rRNA gene sequences, five housekeeping genes, and genome sequences identified Pseudohoeflea suaedae DSM 23348T (98.1 %, 16S rRNA gene sequence similarity) as the most related species to strain DP4N28-3T. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between strain DP4N28-3T and P. suaedae DSM 23348T were all below the threshold of species demarcation. Major phenotypic differences were the flagella type and the limited sources of single carbon utilization by strain DP4N28-3T, which only included acetic acid, acetoacetic acid, d-glucuronic acid, and glucuronamide. Strain DP4N28-3T harboured the class I poly-β-hydroxyalkanoate synthase gene (phaC) and produced poly-β-hydroxybutyrate. The fatty acids were summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c, 49.4 %) and C16 : 0 (13.4 %). The major cellular polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, and sulfoquinovosyl diacylglycerol. The respiratory quinone was Q-10. The results of the phylogenetic, genomic, phenotypic, and chemotaxonomic analysis indicated that the isolated strain represents the type strain of a novel species. Based on these results, strain DP4N28-3T (=MCCC 1K05639T=KCTC 82803T) is proposed as the type strain of the novel species Pseudohoeflea coraliihabitans sp. nov.

Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov., isolated from marine sediment

Two bacterial strains, Y60-23T and HN-65T, were isolated from marine sediment samples collected from Xiaoshi Island, Weihai, and Dongzhai Harbour, Haikou, PR China, respectively. Based on the 16S rRNA gene sequences, strain Y60-23T exhibited 96.0% similarity to its most related type strain Hyphobacterium vulgare KCTC 52487T, while strain HN-65T exhibited 97.3% similarity to its most related type strain Hyphobacterium indicum 2ED5T. The 16S rRNA gene sequence similarity between the two strains was 95.8%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y60-23T and HN-65T belonged to the genus Hyphobacterium. Cells of strains Y60-23T and HN-65T were rod-shaped, Gram-stain-negative, aerobic, non-motile, prosthecate and multiplied by binary fission. The major cellular fatty acids (>10.0%) of strain Y60-23T were C18 : 1  ω7c and C17 : 0, while those of strain HN-65T were iso-C17 : 1  ω9c, iso-C17 : 0 and C18 : 1  ω7c. The major respiratory quinone in both strains was ubiquinone-10 (Q-10) and the major polar lipids were monoglycosyl diglyceride, sulfoquinovosyl diacylglycerol and glucuronopyranosyl diglyceride. The genomic DNA G+C contents of strains Y60-23T and HN-65T were 63.9 and 60.7 mol%, respectively. The average nucleotide identity value between the two strains was 72.1% and the DNA-DNA hybridization value was 18.4%, clearly distinguishing them from each other. According to the results of the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, the two strains represented two novel species within the genus Hyphobacterium, for which the names Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov. were proposed with the type strains Y60-23T (=MCCC 1H01433T=KCTC 8172T) and HN-65T (=MCCC 1H01434T=KCTC 8169T), respectively.

Influence of cadmium and zinc contamination on the sediment microbiome of estuarine and coastal ecosystems in the Southwest Coast of India

Metals and their nanoparticles can induce toxicities that influence the survival of both microorganisms and macroorganisms. The current study reports on the impact of heavy metal pollution on the microbiome of estuarine and coastal sediments, where the settling and final remineralization of organic matter occur. Sediment samples collected from the Cochin estuary along the southwest coast of India and its adjacent coast showed high concentrations of cadmium (Cd) and zinc (Zn). The contamination factor (CF), calculated by comparing the concentration of metals in each station with that of shale value for Cd and Zn, ranged from 5.2 to 8.7 and 1.5 to 2.0 respectively, in the estuarine and coastal stations. Microbiome analysis revealed that bacteria were common across all stations but varied in relative abundance. Proteobacteria, Chloroflexi, Actinobacteria, Desulfobacteria, and Acidobacteria were the major bacterial phylum found in all stations. More than 70% of the bacteria were tolerant to 1 mM concentration of Cd. The findings of our study suggest that metal pollution can influence the microbiome of sediments in the estuaries and coasts. Bacteria with metal tolerance may dominate in polluted areas, but their participation in remineralization may be impaired, as evident in our previous reports. This impairment could ultimately influence the dynamics of the food web and the biogeochemical cycling of nutrients, necessitating further research.

Dongia sedimenti sp. nov., isolated from river sediment

A Gram-stain-negative, non-spore-forming and strictly aerobic bacterial strain, designated R-7T, was isolated from river sediment in Wuxi, Jiangsu, PR China. Cells (1.6-3.8 µm long and 0.6-0.8 µm wide) were slightly curved to straight rods and motile by means of a polar flagellum. The strain grew optimally on Reasoner's 2A medium at 30 °C, pH 7.0 and with 1.0% (w/v) NaCl. Strain R-7T exhibited closest 16S rRNA gene sequence similarities to Dongia mobilis CGMCC 1.7660T (95.4%), D. rigui 04SU4-PT (94.6%) and D. soli D78T (93.8%). The phylogenetic trees based on genomic and 16S rRNA gene sequences showed that strain R-7T was clustered in the genus Dongia. The obtained average nucleotide identity and digital DNA-DNA hybridization values between R-7T and the three type strains of the genus Dongia were 73.4, 72.8 and 72.4% and 19.5, 19.0 and 18.7%, respectively. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, two unidentified aminophospholipids and nine unidentified polar lipids. The major cellular fatty acids (>5% of the total) were cyclo-C19 : 0  ω8c, C16 : 0 and C16 : 0 2-OH. The DNA G+C content was 65.5 mol%. On the basis of the evidence presented in this study, strain R-7T represents a novel species of the genus Dongia, for which the name Dongia sedimenti sp. nov. is proposed, with strain R-7T (=KCTC 8082T=MCCC 1K08805T) as the type strain.

Aerial signaling by plant-associated Streptomyces setonii WY228 regulates plant growth and enhances salt stress tolerance

Plant-associated streptomycetes play important roles in plant growth and development. However, knowledge of volatile-mediated crosstalk between Streptomyces spp. and plants remains limited. In this study, we investigated the impact of volatiles from nine endophytic Streptomyces strains on the growth and development of plants. One versatile strain, Streptomyces setonii WY228, was found to significantly promote the growth of Arabidopsis thaliana and tomato seedlings, confer salt tolerance, and induce early flowering and increased fruit yield following volatile treatment. Analysis of plant growth-promoting traits revealed that S. setonii WY228 could produce indole-3-acetic acid, siderophores, ACC deaminase, fix nitrogen, and solubilize inorganic phosphate. These capabilities were further confirmed through genome sequencing and analysis. Volatilome analysis indicated that the volatile organic compounds emitted from ISP-2 medium predominantly comprised sesquiterpenes and 2-ethyl-5-methylpyrazine. Further investigations showed that 2-ethyl-5-methylpyrazine and sesquiterpenoid volatiles were the primary regulators promoting growth, as confirmed by experiments using the terpene synthesis inhibitor phosphomycin, pure compounds, and comparisons of volatile components. Transcriptome analysis, combined with mutant and inhibitor studies, demonstrated that WY228 volatiles promoted root growth by activating Arabidopsis auxin signaling and polar transport, and enhanced root hair development through ethylene signaling activation. Additionally, it was confirmed that volatiles can stimulate plant abscisic acid signaling and activate the MYB75 transcription factor, thereby promoting anthocyanin synthesis and enhancing plant salt stress tolerance. Our findings suggest that aerial signaling-mediated plant growth promotion and abiotic stress tolerance represent potentially overlooked mechanisms of Streptomyces-plant interactions. This study also provides an exciting strategy for the regulation of plant growth and the improvement of horticultural crop yields within sustainable agricultural practices.

Whole genome-based comparative analysis of the genus Streptomyces reveals many misclassifications

Streptomyces species are experts in the production of bioactive secondary metabolites; however, their taxonomy has fallen victim of the tremendous interest shown by the scientific community, evident in the discovery of numerous synonymous in public repositories. Based on genomic data from NCBI Datasets and nomenclature from the LPSN database, we compiled a dataset of 600 Streptomyces species along with their annotations and metadata. To pinpoint the most suitable taxonomic classification method, we conducted a comprehensive assessment comparing multiple methodologies, including analysis of 16S rRNA, individual housekeeping genes, multilocus sequence analysis (MLSA), and Fast Average Nucleotide Identity (FastANI) on a subset of 409 species with complete data. Due to insufficient resolution of 16S rRNA and inconsistency observed in individual housekeeping genes, we performed a more in-depth analysis, comparing only FastANI and MLSA, which expanded our dataset to include 502 species. With FastANI validated as the preferred method, we conducted pairwise analysis on the entire dataset identifying 59 non-unique species among the 600, and subsequently refined the dataset to 541 unique species. Additionally, we collected data on 724 uncharacterized Streptomyces strains to investigate the uniqueness potential of the unannotated fraction of the Streptomyces genus. Utilizing FastANI, 289 strains could be successfully classified into one of the 541 Streptomyces species. KEY POINTS: • Evaluation of taxonomic classification methods for Streptomyces species. • Whole genome analysis, specifically FastANI, has been chosen as preferred method. • Various reclassifications are proposed within the Streptomyces genus.

Biodegradation of Cyromazine by Mycobacterium sp. M15: Performance, Degradation Pathways, and Key Enzymes

Cyromazine, a triazine insecticide, raises food safety concerns due to residues in vegetables like cowpeas. Microbial metabolism is key for pesticide elimination, but bacteria efficient in cyromazine degradation are limited, with uncharacterized enzymes. This study isolated a highly efficient cyromazine-degrading bacterium, Mycobacterium sp. M15, from a cowpea field. M15 utilized cyromazine as the sole carbon source for its growth and completely degraded 0.5 mM cyromazine within 24 h. The degradation pathway involved hydrolyzing cyromazine to N-cyclopropylammeline and further to N-cyclopropylammelide, with amino groups removed sequentially. The cyclopropylamine group in N-cyclopropionamide continued to hydrolyze to cyanuric acid. A protein, CriA, identified as an aminohydrolase in M15, degraded cyromazine to N-cyclopropylammeline. Using CriA reduced cyromazine residues on cowpea surfaces and completely degraded them in immersion solutions. These findings offer insights into cyromazine's microbial degradation mechanism and highlight the potential of cyromazine-degrading enzymes in enhancing food safety.

Reproducible chemostat cultures to minimize eukaryotic viruses from fecal transplant material

Recent studies indicate an important role of bacteriophages for successful fecal microbiota transplantation (FMT). However, wider clinical applications of FMT are hampered by to donor variability and concerns of infection risks by bacteria and human viruses. To overcome these challenges, mouse cecal and human fecal material were propagated in a chemostat fermentation setup supporting multiplication of bacteria, and phages, while propagation of eukaryotic viruses will be prevented in the absence of eukaryotic host cells. The results showed decrease of the median relative abundance of viral contigs of classified eukaryotic viruses below 0.01%. The corresponding virome profiles showed dilution rate dependency, a reproducibility between biological replicates, and maintained high diversity regarding both the human and mouse inocula. This proof-of-concept cultivation approach may constitute the first step of developing novel therapeutic tools with high reproducibility and with low risk of infection from the donor material to target gut-related diseases.

Patulibacter defluvii sp. nov., Isolated from a Wastewater Treatment Plant in Guangzhou City, China

A novel Gram-stain-positive, aerobic, catalase-positive, oxidase-negative, non-motile, and rod-shaped bacterium with ibuprofen-degrading capacity, designated DM4T, was isolated from the sewage of a wastewater treatment plant (WWTP) in Guangzhou city, China. Strain DM4T grew optimally at 0% (w/v) NaCl, pH 5.0-7.0, and 30 °C, forming white colonies on trypticase soy agar. C18:1ω9c, C18:2ω9.12c and C15:1ω10c were the predominant fatty acids. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain DM4T belonged to the genus Patulibacter, was closely related to Patulibacter medicamentivorans DSM 25692T (98.5%) and P. brassicae KCTC 39817T (98.1%). Strain DM4T had a genome size of 5.33Mbp, and the DNA G + C content was 75.0%. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridisation (dDDH) values between strain DM4T and P. medicamentivorans were 85.2%, 83.9%, and 29.0% respectively, while those between strain DM4T and P. brassicae were 78.5%, 71.3%, and 22.2%, respectively. Strain DM4T could significantly degrade ibuprofen by almost 80% after 84 h of incubation, and the degradation kinetics was well fitted with the first-order kinetics. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain DM4T (= GDMCC 1.4574T = KCTC 59145T) represents a new species of the genus Patulibacter, for which the name Patulibacter defluvii sp. nov. is proposed.

Bioprospecting of extremophilic perchlorate-reducing bacteria: report of promising Bacillus spp. isolated from sediments of the bay of Cartagena, Colombia

Three extremophile bacterial strains (BBCOL-009, BBCOL-014 and BBCOL-015), capable of degrading high concentrations of perchlorate at a range of pH (6.5 to 10.0), were isolated from Colombian Caribbean Coast sediments. Morphological features included Gram negative strain bacilli with sizes averaged of 1.75 × 0.95, 2.32 × 0.65 and 3.08 × 0.70 μm, respectively. The reported strains tolerate a wide range of pH (6.5 to 10.0); concentrations of NaCl (3.5 to 7.5% w/v) and KClO4- (250 to 10000 mg/L), reduction of KClO4- from 10 to 25%. LB broth with NaCl (3.5-30% w/v) and KClO4- (250-10000 mg/L) were used in independent trials to evaluate susceptibility to salinity and perchlorate, respectively. Isolates increased their biomass at 7.5 % (w/v) NaCl with optimal development at 3.5 % NaCl. Subsequently, ClO4- reduction was assessed using LB medium with 3.5% NaCl and 10000 mg/L ClO4-. BBCOL-009, BBCOL-014 and BBCOL-015 achieved 10%, 17%, and 25% reduction of ClO4-, respectively. The 16 S rRNA gene sequence grouped them as Bacillus flexus T6186-2, Bacillus marisflavi TF-11 (T), and Bacillus vietnamensis 15 - 1 (T) respectively, with < 97.5% homology. In addition, antimicrobial resistance to ertapenem, vancomycine, amoxicillin clavulanate, penicillin, and erythromycin was present in all the isolates, indicating their high adaptability to stressful environments. The isolated strains from marine sediments in Cartagena Bay, Colombia are suitable candidates to reduce perchlorate contamination in different environments. Although the primary focus of the study of perchlorate-reducing and resistant bacteria is in the ecological and agricultural realms, from an astrobiological perspective, perchlorate-resistant bacteria serve as models for astrobiological investigations.

Gilvirhabdus luticola gen. nov., sp. nov., a mesophilic and halophilic bacterium isolated from tidal flat sediment

Two novel bacteria, MJ-SS3T and MJ-SS4, were isolated from tidal flat sediment sampled in Gochang, Republic of Korea. The isolates were Gram-stain-negative, aerobic, non-motile, rod-shaped, yellow-coloured, oxidase-positive, and catalase-positive. Strains MJ-SS3T and MJ-SS4 grew at 20-37 °C (optimum, 30 °C), at pH 6-8 (optimum, pH 7.0) and in the presence of 0-7 % (w/v) NaCl (optimum, 2.0 % NaCl). Strains MJ-SS3T and MJ-SS4 showed 99.9 % 16S rRNA gene sequence similarity. Phylogenetic analysis based on genome and 16S rRNA gene sequences indicated that strains MJ-SS3T and MJ-SS4 were affiliated with the family Flavobacteriaceae and most closely related to Formosa maritima 1494T (95.3 %), Hanstruepera flava NBU2984T (95.2 %), Yeosuana marina JLT21T (95.2 %), Meridianimaribacter flavus NH57NT (95.1 %), and Geojedonia litorea YCS-16T (95.1 %). The major respiratory quinone was menaquinone-6. The major identified polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, and amino lipids. The major cellular fatty acids of strain MJ-SS3T were iso-C15 : 1 G (24.6 %), iso-C15 : 0 (21.6 %), and iso-C17 : 0 3-OH (15.8 %). The genome length of strain MJ-SS3T is 3.1 Mbp (DNA G+C content, 32.5 mol%) and it has 2822 coding and 59 tRNA genes. The average amino acid identity and average nucleotide identity values, as well as biochemical, phylogenetic, and physiological characteristics, strongly supported the genotypic and phenotypic differentiation of strains MJ-SS3T and MJ-SS4 from other members of the family Flavobacteriaceae. Hence, strains MJ-SS3T and MJ-SS4 are considered to represent a novel species of a new genus in the family Flavobacteriaceae, for which the Gilvirhabdus luticola gen. nov., sp. nov. is proposed. The type strain is MJ-SS3T (=KCTC 102114T=KEMB 20189T=JCM 36595T), with reference strain MJ-SS4 (=KCTC 102115=KEMB 20190).

Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet Hot Springs, China

Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus in geographically different thermal springs. Sixteen Thermus strains were isolated and sequenced from hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of 971 Orthologous Protein Families (supermatrix and gene content methods) revealed a mixed distribution of the Thermus strains. Whole genome based phylogenetic analysis showed, all 16 Thermus strains belong to five species; Thermus oshimai (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), Thermus antranikianii (YIM 73052, 77412, 77311, 71206), Thermus brokianus (YIM 73518, 71318, 72351), Thermus hydrothermalis (YIM 730264 and 77927) and one potential novel species 77420 forming clade with Thermus thalpophilus SYSU G00506T. Although the genomes of different strains of Thermus of same species were highly similar in their metabolic pathways, but subtle differences were found. CRISPR loci were detected through genome-wide screening, which showed that Thermus isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the Thermus genomes which could be helpful to acquire DNA from environment. In the present study it was found that Thermus isolates use two mechanism of incomplete denitrification pathway, some Thermus strains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of Thermus genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of T. oshimai and T. antranikianii strains, while genomes of all T. brokianus strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced Thermus strains. Strains 77,420, 77,311, 73,518, 77,412 and 72,351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy. Through the comparative genomic analysis, we also identified 77420 as the genome type species and its validity as novel organism was confirmed by whole genome sequences comparison. Although isolate 77420 had 99.0% 16S rRNA gene sequence similarity with T. thalpophilus SYSU G00506T but based on ANI 95.86% (Jspecies) and digital DDH 68.80% (GGDC) values differentiate it as a potential novel species. Similarly, in the phylogenomic tree, the novel isolate 77,420 forming a separate branch with their closest reference type strain T. thalpophilus SYSU G00506T.

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments

BACKGROUND

Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinder their wider clinical application in treating less acute diseases.

METHODS

To overcome these challenges, we developed methods to broaden FVT's clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: (1) chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), (2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and (3) pyronin-Y treatment to inhibit RNA virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in a C. difficile infection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline.

RESULTS

FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to FMT, FVT-PyT, and saline (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizing C. difficile cells and associated toxin A/B levels. There was a potential elimination of C. difficile colonization, with seven out of eight mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence of C. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels, and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy.

CONCLUSIONS

This proof-of-concept study shows that specific modifications of FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limiting C. difficile colonization in mice, with solvent/detergent treatment and chemostat propagation of donor phages emerging as promising approaches. Video Abstract.