Life | Topical Collection : Isolation and Characterization of New Microbial Species and Strains

2025

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22 pages, 3547 KiB

Open AccessArticle

Hypoglycemic, Antioxidant Activities, and Probiotic Characteristics of Lacticaseibacillus rhamnosus LBUX2302 Isolated from Stool Samples of Neonates

by Pedro A. Reyes-Castillo, Ana Laura Esquivel-Campos, Edgar Torres-Maravilla, Eduardo Zúñiga-León, Felipe Mendoza-Pérez, Rosa González-Vázquez, María Guadalupe Córdova-Espinoza, María Angélica Gutiérrez-Nava, Raquel González-Vázquez and Lino Mayorga-Reyes

Life 2025, 15(5), 804; https://doi.org/10.3390/life15050804 - 18 May 2025

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Abstract

Lacticaseibacillus species have shown potential in managing hyperglycemia, hypercholesterolemia, and oxidative stress, depending on the strain and species. This study aimed to isolate a novel Lacticaseibacillus rhamnosus strain from healthy newborns and assess its hypoglycemic and antioxidative activity, along with other probiotic properties. [...] Read more.

Lacticaseibacillus species have shown potential in managing hyperglycemia, hypercholesterolemia, and oxidative stress, depending on the strain and species. This study aimed to isolate a novel Lacticaseibacillus rhamnosus strain from healthy newborns and assess its hypoglycemic and antioxidative activity, along with other probiotic properties. A non-hemolytic L. rhamnosus LBUX2302 was isolated, and it exhibited survival rates of 2.7%, 22%, and 27.5% at pH 2, 3, and 5 for 120 min. It metabolized various carbon sources and showed resistance to gentamicin, dicloxacillin, and penicillin; coaggregated with Salmonella typhi ATCC14028, Staphylococcus aureus STCC6538, and Escherichia coli O157:H7. L. rhamnosus LBUX2302 showed hydrophobicity, autoaggregation, and adhesion to HaCat, HeLa, MCF-7, SK-LU-1, and SW620 cell lines. It also exhibited extracellular activity of bile salt hydrolase. Enzymatic inhibition assays revealed 66% and 24% inhibitions of α-amylase and α-glucosidase, respectively. Its cell-free supernatant inhibited DPPH (89%), hydroxyl (81%), and superoxide anion radicals (61%). Also, antioxidant activity was observed in whole cells and cell fragments. Finally, the presence of ferulic acid activity was detected. The results highlight L. rhamnosus LBUX2302 as a promising probiotic with hypoglycemic and antioxidant effects, warranting further in vivo evaluation for its possible inclusion in functional food and health formulations. Full article

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21 pages, 8909 KiB

Open AccessArticle

Isolation, Sphalerite Bioleaching, and Whole Genome Sequencing of Acidithiobacillus ferriphilus QBS3 from Zinc-Rich Sulfide Mine Drainage

by Kan Wang, Yuandong Liu, Run Liu, Wissal Belqadi, Weimin Zeng, Runlan Yu and Xueling Wu

Life 2025, 15(5), 792; https://doi.org/10.3390/life15050792 - 15 May 2025

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Abstract

The genus Acidithiobacillus has been widely used in bioleaching, and novel strains in this genus, such as A. ferriphilus, have also been confirmed to possess bioleaching capabilities. In this study, an Acidithiobacillus ferriphilus strain, QBS3, was isolated from zinc-rich sulfide mine drainage [...] Read more.

The genus Acidithiobacillus has been widely used in bioleaching, and novel strains in this genus, such as A. ferriphilus, have also been confirmed to possess bioleaching capabilities. In this study, an Acidithiobacillus ferriphilus strain, QBS3, was isolated from zinc-rich sulfide mine drainage using the gradient dilution method. QBS3 is a Gram-negative, 1.3 µm rod-shaped bacterium with small red colonies. It showed a high iron oxidation efficiency of 0.361 g/(L·h) and a sulfur oxidation efficiency of 0.206 g/(L·d). QBS3 has sphalerite bioleaching ability; using QBS3 for pure sphalerite bioleaching, 18.8% of zinc was extracted in 14 days at 1% pulp density. Whole genome sequencing was performed on QBS3. Functional prediction showed that 9.13% of the genes were involved in replication, recombination, and repair. Bioleaching-related genes were analyzed, including iron and sulfur oxidation genes, and carbon and nitrogen fixation genes. For iron oxidation, the Cyc2→RusA pathway and Iro→RusB pathway were found in QBS3. In terms of sulfur oxidation, QBS3 has an incomplete SOX system and lacks the SDO gene, but Rho and Trx may complement the SOX system, enabling QBS3 to oxidize sulfur. QBS3 has multiple sets of carbon fixation genes, and nitrogen fixation genes were also identified. A hypothetical sphalerite bioleaching model is proposed; this study provides a theoretical basis for the zinc sulfide ore bioleaching industry. Full article

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14 pages, 5593 KiB

Open AccessArticle

Phenotypic and Genomic Characterization of Oceanisphaera submarina sp. nov. Isolated from the Sea of Japan Bottom Sediments

by Lyudmila Romanenko, Evgeniya Bystritskaya, Nadezhda Otstavnykh, Valeriya Kurilenko, Peter Velansky and Marina Isaeva

Life 2025, 15(3), 378; https://doi.org/10.3390/life15030378 - 27 Feb 2025

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Abstract

A Gram-negative aerobic, motile bacterium KMM 10153^T was isolated from bottom sediment sampled from the Sea of Japan at a depth of 256 m, Russia. Strain KMM 10153^T grew in 0–12% NaCl at temperatures ranging from 4 to 42 °C and [...] Read more.

A Gram-negative aerobic, motile bacterium KMM 10153^T was isolated from bottom sediment sampled from the Sea of Japan at a depth of 256 m, Russia. Strain KMM 10153^T grew in 0–12% NaCl at temperatures ranging from 4 to 42 °C and produced brown diffusible pigments. Based on the 16S rRNA gene and whole genome sequences analyses, novel bacterium KMM 10153^T was affiliated with the genus Oceanisphaera (phylum Pseudomonadota) showing the highest 16S rRNA gene sequence similarities of 98.94% to Oceanisphaera arctica KCTC 23013^T, 98.15% to Oceanisphaera donghaensis BL1^T, and similarity values of <98% to other validly described Oceanisphaera species. The pairwise Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) values between the novel strain KMM 10153^T and the three closest type strains Oceanishaera arctica KCTC 23013^T, Oceanisphaera litoralis DSM 15406^T and Oceanisphaera sediminis JCM 17329^T were 89.4%, 89.1%, 87.41%, and 90.7%, 89.8%, 89.7%, respectively. The values of digital DNA–DNA hybridization (dDDH) were below 39.3%. The size of the KMM 10153^T draft genome was 3,558,569 bp, and the GC content was 57.5%. The genome of KMM 10153^T harbors 343 unique genes with the most abundant functional classes consisting of transcription, mobilome, amino acid metabolism, and transport. Strain KMM 10153^T contained Q-8 as the predominant ubiquinone and C_16:1ω7c, C_16:0, and C_18:1ω7c as the major fatty acids. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidic acid. Based on the distinctive phenotypic characteristics and the results of phylogenetic and genomic analyses, the marine bacterium KMM 10153^T could be classified as a novel Oceanisphaera submarina sp. nov. The type strain of the species is strain KMM 10153^T (=KCTC 8836^T). Full article

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15 pages, 3682 KiB

Open AccessArticle

Paracoccus broussonetiae subsp. drimophilus subsp. nov., a Novel Subspecies Salt-Tolerant Endophytic Bacterium from Maize Root in Hunan

by Xue Li, Chi Zhou, Ming Li, Qingzhuang Zhang, Lei Su and Xin Li

Life 2025, 15(3), 354; https://doi.org/10.3390/life15030354 - 24 Feb 2025

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Abstract

In an investigation exploring endophytic microbiota from agricultural crops, an aerobic, non-motile, Gram-negative, coccobacillus-shaped bacterial isolate, designated as strain NGMCC 1.201697^T, was isolated from maize roots in Hunan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain [...] Read more.

In an investigation exploring endophytic microbiota from agricultural crops, an aerobic, non-motile, Gram-negative, coccobacillus-shaped bacterial isolate, designated as strain NGMCC 1.201697^T, was isolated from maize roots in Hunan Province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NGMCC 1.201697^T belonged to the genus Paracoccus, showing the highest sequence similarity to Paracoccus broussonetiae CPCC 101403^T (99.86%). The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) were 98.57% and 87.90% between the novel isolate and its closest phylogenetic relative. However, phenotypic characterization further differentiated the isolate from P. broussonetiae CPCC 101403^T. The isolate showed enhanced environmental tolerance adaptability (growth in 0–8% NaCl and 4–37 °C), unique enzymatic activities (esterase C4, β-glucosidase, L-proline arylamidase, and β-galactosidase), and expanded metabolic capabilities (D-mannitol, D-cellobiose, saccharose, and so on). The major polar lipids consisted of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), two unidentified glycolipids (GLs) and four unidentified phospholipids (PLs). The predominant respiratory quinone was ubiquinone-10, and the major fatty acid was summed feature 8 (C18:1 ω7c, 69.42%). The DNA G + C content was 64.49 mol%. Based on results of these analyses, strain NGMCC 1.201697^T represents a novel subspecies of Paracoccus broussonetiae, for which the name Paracoccus broussonetiae subsp. drimophilus subsp. nov. is proposed. The type-strain is NGMCC 1.201697^T (=CGMCC 1.61958^T =JCM 37104^T). Full article

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18 pages, 3263 KiB

Open AccessArticle

Description and Comparative Genomics of Algirhabdus cladophorae gen. nov., sp. nov., a Novel Aerobic Anoxygenic Phototrophic Bacterial Epibiont Associated with the Green Alga Cladophora stimpsonii

by Olga Nedashkovskaya, Sergey Baldaev, Alexander Ivaschenko, Evgenia Bystritskaya, Natalia Zhukova, Viacheslav Eremeev, Andrey Kukhlevskiy, Valeria Kurilenko and Marina Isaeva

Life 2025, 15(3), 331; https://doi.org/10.3390/life15030331 - 21 Feb 2025

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Abstract

A novel, strictly aerobic, non-motile, and pink-pigmented bacterium, designated 7Alg 153^T, was isolated from the Pacific green alga Cladophora stimpsonii. Strain 7Alg 153^T was able to grow at 4–32 °C in the presence of 1.5–4% NaCl and hydrolyze L-tyrosine, gelatin, [...] Read more.

A novel, strictly aerobic, non-motile, and pink-pigmented bacterium, designated 7Alg 153^T, was isolated from the Pacific green alga Cladophora stimpsonii. Strain 7Alg 153^T was able to grow at 4–32 °C in the presence of 1.5–4% NaCl and hydrolyze L-tyrosine, gelatin, aesculin, Tweens 20, 40, and 80 and urea, as well as produce catalase, oxidase, and nitrate reductase. The novel strain 7Alg 153^T showed the highest similarity of 96.75% with Pseudaestuariivita rosea H15^T, followed by Thalassobius litorarius MME-075^T (96.60%), Thalassobius mangrovi GS-10^T (96.53%), Tritonibacter litoralis SM1979^T (96.45%), and Marivita cryptomonadis CL-SK44^T (96.38%), indicating that it belongs to the family Roseobacteraceae, the order Rhodobacteales, the class Alphaproteobacteria, and the phylum Pseudomonadota. The respiratory ubiquinone was Q-10. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, and one unidentified lipid. The predominant cellular fatty acids (>5%) were C_18:1 ω7c, C_16:0, C_18:0, and 11-methyl C_18:1 ω7c. The 7Alg 153^T genome is composed of a single circular chromosome of 3,786,800 bp and two circular plasmids of 53,157 bp and 37,459 bp, respectively. Pan-genome analysis showed that the 7Alg 153^T genome contains 33 genus-specific clusters spanning 92 genes. The COG20-annotated singletons were more often related to signal transduction mechanisms, cell membrane biogenesis, transcription, and transport, and the metabolism of amino acids. The complete photosynthetic gene cluster (PGC) for aerobic anoxygenic photosynthesis (AAP) was found on a 53 kb plasmid. Based on the phylogenetic evidence and phenotypic and chemotaxonomic characteristics, the novel isolate represents a novel genus and species within the family Roseobacteraceae, for which the name Algirhabdus cladophorae gen. nov., sp. nov. is proposed. The type strain is 7Alg 153^T (=KCTC 72606^T = KMM 6494^T). Full article

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2024

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3 pages, 132 KiB

Open AccessEditorial

Advancing Microbiology through the Discovery of New Microbial Species and Strains

by Pabulo Henrique Rampelotto

Life 2024, 14(5), 626; https://doi.org/10.3390/life14050626 - 13 May 2024

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Abstract

In our pursuit of understanding the intricacies of microbial life, the isolation and characterization of new microbial species and strains play a pivotal role [...] Full article

14 pages, 3071 KiB

Open AccessArticle

Peloplasma aerotolerans gen. nov., sp. nov., a Novel Anaerobic Free-Living Mollicute Isolated from a Terrestrial Mud Volcano

by Maria A. Khomyakova, Alexander Y. Merkel, Andrei A. Novikov and Alexander I. Slobodkin

Life 2024, 14(5), 563; https://doi.org/10.3390/life14050563 - 26 Apr 2024

Cited by 2 | Viewed by 1388

Abstract

A novel aerotolerant anaerobic bacterium (strain M4Ah^T) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells were small, cell-wall-less, non-motile cocci, 0.32–0.65 μm in diameter. The isolate was a mesophilic, neutrophilic chemoorganoheterotroph, growing on carbohydrates (D-glucose, D-trehalose, D-ribose, D-mannose, [...] Read more.

A novel aerotolerant anaerobic bacterium (strain M4Ah^T) was isolated from a terrestrial mud volcano (Taman Peninsula, Russia). Cells were small, cell-wall-less, non-motile cocci, 0.32–0.65 μm in diameter. The isolate was a mesophilic, neutrophilic chemoorganoheterotroph, growing on carbohydrates (D-glucose, D-trehalose, D-ribose, D-mannose, D-xylose, D-maltose, D-lactose, D-cellobiose, D-galactose, D-fructose, and D-sucrose), proteinaceous compounds (yeast extract, tryptone), and pyruvate. Strain M4Ah^T tolerated 2% oxygen in the gas phase, was catalase-positive, and showed sustainable growth under microaerobic conditions. The dominant cellular fatty acids of strain M4Ah^T were C_16:0 and C_18:0. The G+C content of the genomic DNA was 32.42%. The closest phylogenetic relative of strain M4Ah^T was Mariniplasma anaerobium from the family Acholeplasmataceae (order Acholeplasmatales, class Mollicutes). Based on the polyphasic characterization of the isolate, strain M4Ah^T is considered to represent a novel species of a new genus, for which the name Peloplasma aerotolerans gen. nov., sp. nov. is proposed. The type strain of Peloplasma aerotolerans is M4Ah^T (=DSM 112561^T = VKM B-3485^T = UQM 41475^T). This is the first representative of the order Acholeplasmatales, isolated from a mud volcano. Full article

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14 pages, 7735 KiB

Open AccessArticle

Draft Genome Sequence Analyses of Two Novel Marinobacter suadae sp. nov. and Wenyingzhuangia gilva sp. nov. Isolated from the Root of Suaeda japonica Makino

by Sunho Park, Inhyup Kim, Geeta Chhetri, Yonghee Jung, Haejin Woo and Taegun Seo

Life 2024, 14(3), 296; https://doi.org/10.3390/life14030296 - 22 Feb 2024

Cited by 1 | Viewed by 1677

Abstract

Gram-negative, rod-shaped, and aerobic bacteria designated chi1^T and chi5^T were isolated from the root of Suaeda japonica Makino. Phylogenetics utilizing 16S rRNA and whole-genome sequences of the two novel strains chi1^T and chi5^T confirmed that they were related to [...] Read more.

Gram-negative, rod-shaped, and aerobic bacteria designated chi1^T and chi5^T were isolated from the root of Suaeda japonica Makino. Phylogenetics utilizing 16S rRNA and whole-genome sequences of the two novel strains chi1^T and chi5^T confirmed that they were related to the genera Marinobacter and Wenyingzhuangia, respectively. For the novel strains chi1^T and chi5^T, the digital DNA–DNA hybridization values (19–20% and 22.1–36.6%, respectively) and average nucleotide identity values (74.4–76.5% and 79.1–88.9%, respectively) fell within the range for the genera Marinobacter and Wenyingzhuangia, respectively. Pangenome analyses of the novel strains chi1^T and chi5^T revealed 357 and 368 singletons genes, respectively. The genomic DNA G + C contents of the strains chi1^T and chi5^T were 57.2% and 31.5%, respectively. The major fatty acids of strain chi1^T were C_12:0, C_16:0, and summed feature 3 (C_16:1 ω6c and/or C_16:1ω7c), while those of the strain chi5^T were iso-C_15:0 3OH, iso-C_17:0 3OH, and iso-C_15:0. Data from the phylogenetic, phylogenomic, pangenome, genomic, physiological, and biochemical analyses indicated that the novel strains were distinct. Therefore, we propose the names Marinobacter suadae (type strain chi1^T = KACC 23259^T = TBRC 17652^T) and Wenyingzhangia gilva (type strain chi5^T = KACC 23262^T = TBRC 17900^T) for the studied bacterial strains. Full article

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14 pages, 4543 KiB

Open AccessArticle

Isolation and Characterization of Mycoplasma ovipneumoniae Infecting Goats with Pneumonia in Anhui Province, China

by Jiahong Chen, Shijia Wang, Dong Dong, Zijun Zhang, Yafeng Huang and Yong Zhang

Life 2024, 14(2), 218; https://doi.org/10.3390/life14020218 - 2 Feb 2024

Cited by 1 | Viewed by 2656

Abstract

Mycoplasma ovipneumoniae (M. ovipneumoniae) causes a fatal infection in goats, leading to significant economic losses in the small-ruminant industry worldwide. The present study aimed to characterize the strains of M. ovipneumoniae infecting goats with pneumonia in Anhui Province, China. From November [...] Read more.

Mycoplasma ovipneumoniae (M. ovipneumoniae) causes a fatal infection in goats, leading to significant economic losses in the small-ruminant industry worldwide. The present study aimed to characterize the strains of M. ovipneumoniae infecting goats with pneumonia in Anhui Province, China. From November 2021 to January 2023, among 20 flocks, a total of 1320 samples (600 samples of unvaccinated blood, 400 nasal swabs, 200 samples of pleural fluid, and 120 samples of lung tissue) were obtained from goats with typical signs of pneumonia, such as a low growth rate, appetite suppression, increased temperature, discharge from the nose, and a cough. Necropsied goats showed increased pleural fluid, fibrinous pleuropneumonia, and attached localized pleural adhesions. M. ovipneumoniae isolated from the samples were subjected to an indirect hemagglutination test (IHA), PCR amplicon sequencing, phylogenetic analysis, and biochemical identification tests. The overall positivity rate of M. ovipneumoniae was 27.50%. Mycoplasmas were obtained from 80 (20.0%) nasal swabs, 21 (10.5%) pleural fluid samples, and 15 (12.5%) lung samples. PCR amplicon (288 bp) sequencing identified eight strains of M. ovipneumoniae. In a phylogenetic tree, the isolated strains were homologous to the standard strain M. ovipneumoniae Y-98 and most similar to M. ovipneumoniae FJ-SM. Local strains of M. ovipneumoniae were isolated from goats in Anhui province. The identified genomic features and population structure will promote further study of M. ovipneumoniae pathogenesis and could form the basis for vaccine and therapy development. Full article

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