Microbacterium album sp. nov. and Microbacterium deserti sp. nov., two halotolerant actinobacteria isolated from desert soil

Microbacterium horticulturae sp. nov., a novel actinobacterium isolated from flowerpot soil

Strain CJN36-1NT, a Gram-stain-positive, non-flagellated, strictly aerobic and short rod-shaped bacterium, was isolated from flowerpot soil sampled in the Jeonju region of the Republic of Korea. Based on 16S rRNA gene sequences and the resulting phylogenetic tree, the strain belonged to the genus Microbacterium. Strain CJN36-1NT contained a chromosome of 3.6 Mbp with a G+C content of 68.5 mol%. The strain grew at 10-37 °C (optimally at 28 °C), at pH 5.0-8.0 (optimally at pH 8.0), and in the presence of 0-7 % NaCl (w/v; optimally with 0 % NaCl). Digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values between strain CJN36-1NT and its closest related species, Microbacterium protaetiae DFW100M-13T, were 82.0, 81.2, and 23.2 %, respectively. We propose naming this novel species Microbacterium horticulturae sp. nov., with CJN36-1NT (=KACC 23027T=NBRC 116065T) as the type strain.

Microbacterium elymi sp. nov., Isolated from the Rhizospheric Soil of Elymus tsukushiensis, a Plant Native to the Dokdo Islands, Republic of Korea

Microbacterium elymi KUDC0405^T was isolated from the rhizosphere of Elymus tsukushiensis from the Dokdo Islands. The KUDC0405^T strain was Gram-stain-positive, non-spore forming, non-motile, and facultatively anaerobic bacteria. Strain KUDC0405^T was a rod-shaped bacterium with size dimensions of 0.3-0.4 × 0.7-0.8 μm. Based on 16S rRNA gene sequences, KUDC0405^T was most closely related to Microbacterium bovistercoris NEAU-LLE^T (97.8%) and Microbacterium pseudoresistens CC-5209^T (97.6%). The dDDH (digital DNA-DNA hybridization) values between KUDC0405^T and M. bovistercoris NEAU-LLE^T and M. pseudoresistens CC-5209^T were below 17.3% and 17.5%, respectively. The ANI (average nucleotide identity) values among strains KUDC0405^T, M. bovistercoris NEAU-LLE^T, and M. pseudoresistens CC-5209^T were 86.6% and 80.7%, respectively. The AAI (average amino acid identity) values were 64.66% and 64.97%, respectively, between KUDC0405^T and its closest related type strains. The genome contained 3,596 CDCs, three rRNAs, 46 tRNAs, and three non-coding RNAs (ncRNAs). The genomic DNA GC content was 70.4%. The polar lipids included diphosphatydilglycerol, glycolipid, phosphatydilglycerol, and unknown phospholipid, and the major fatty acids were anteiso-C_17:0 and iso-C_16:0. Strain KUDC0405^T contained MK-12 as the major menaquinone. Based on genotypic, phylogenetic, and phenotypic properties, strain KUDC0405^T should be considered a novel species within the genus Microbacterium, for which we propose the name M. elymi sp. nov., and the type strain as KUDC0405^T (=KCTC 49411^T, =CGMCC1.18472^T).

Sweat and Sebum Preferences of the Human Skin Microbiota

The microorganisms inhabiting human skin must overcome numerous challenges that typically impede microbial growth, including low pH, osmotic pressure, and low nutrient availability. Yet the skin microbiota thrive on the skin and have adapted to these stressful conditions. The limited nutrients available for microbial use in this unique niche include those from host-derived sweat, sebum, and corneocytes. Here, we have developed physiologically relevant, synthetic skin-like growth media composed of compounds present in sweat and sebum. We find that skin-associated bacterial species exhibit unique growth profiles at different concentrations of artificial sweat and sebum. Most strains evaluated demonstrate a preference for high sweat concentrations, while the sebum preference is highly variable, suggesting that the capacity for sebum utilization may be a driver of the skin microbial community structure. In particular, the prominent skin commensal Staphylococcus epidermidis exhibits the strongest preference for sweat while growing equally well across sebum concentrations. Conversely, the growth of Corynebacterium kefirresidentii, another dominant skin microbiome member, is dependent on increasing concentrations of both sweat and sebum but only when sebum is available, suggesting a lipid requirement of this species. Furthermore, we observe that strains with similar growth profiles in the artificial media cluster by phylum, suggesting that phylogeny is a key factor in sweat and sebum use. Importantly, these findings provide an experimental rationale for why different skin microenvironments harbor distinct microbiome communities. In all, our study further emphasizes the importance of studying microorganisms in an ecologically relevant context, which is critical for our understanding of their physiology, ecology, and function on the skin. IMPORTANCE The human skin microbiome is adapted to survive and thrive in the harsh environment of the skin, which is low in nutrient availability. To study skin microorganisms in a system that mimics the natural skin environment, we developed and tested a physiologically relevant, synthetic skin-like growth medium that is composed of compounds found in the human skin secretions sweat and sebum. We find that most skin-associated bacterial species tested prefer high concentrations of artificial sweat but that artificial sebum concentration preference varies from species to species, suggesting that sebum utilization may be an important contributor to skin microbiome composition. This study demonstrates the utility of a skin-like growth medium, which can be applied to diverse microbiological systems, and underscores the importance of studying microorganisms in an ecologically relevant context.

Actinobacteria From Desert: Diversity and Biotechnological Applications

Deserts, as an unexplored extreme ecosystem, are known to harbor diverse actinobacteria with biotechnological potential. Both multidrug-resistant (MDR) pathogens and environmental issues have sharply raised the emerging demand for functional actinobacteria. From 2000 to 2021, 129 new species have been continuously reported from 35 deserts worldwide. The two largest numbers are of the members of the genera Streptomyces and Geodermatophilus, followed by other functional extremophilic strains such as alkaliphiles, halotolerant species, thermophiles, and psychrotolerant species. Improved isolation strategies for the recovery of culturable and unculturable desert actinobacteria are crucial for the exploration of their diversity and offer a better understanding of their survival mechanisms under extreme environmental stresses. The main bioprospecting processes involve isolation of target actinobacteria on selective media and incubation and selection of representatives from isolation plates for further investigations. Bioactive compounds obtained from desert actinobacteria are being continuously explored for their biotechnological potential, especially in medicine. To date, there are more than 50 novel compounds discovered from these gifted actinobacteria with potential antimicrobial activities, including anti-MDR pathogens and anti-inflammatory, antivirus, antifungal, antiallergic, antibacterial, antitumor, and cytotoxic activities. A range of plant growth-promoting abilities of the desert actinobacteria inspired great interest in their agricultural potential. In addition, several degradative, oxidative, and other functional enzymes from desert strains can be applied in the industry and the environment. This review aims to provide a comprehensive overview of desert environments as a remarkable source of diverse actinobacteria while such rich diversity offers an underexplored resource for biotechnological exploitations.

Microbacterium stercoris sp. nov., an indole acetic acid-producing actinobacterium isolated from cow dung

A novel growth-promoting and indole acetic acid-producing strain, designated NEAU-LLB^T, was isolated from cow dung collected from Shangzhi, Heilongjiang Province, PR China. Cells of strain NEAU-LLB^T were Gram-stain-positive, non-motile, aerobic and non-spore-forming. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NEAU-LLB^T belonged to the genus Microbacterium. Strain NEAU-LLB^T had high 16S rRNA sequence similarities of 98.81 and 98.41 % to Microbacterium paludicola DSM 16915^T and Microbacterium marinilacus DSM 18904^T, and less than 98 % to other members of the genus Microbacterium. Chemotaxonomic characteristics showed that MK-11 and MK-12 were detected as the predominant menaquinones. The peptidoglycan contained glutamic acid, aspartic acid, glycine, ornithine and a small amount of alanine, with ornithine as the diagnostic diamino acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The major fatty acids were identified as anteiso-C_15 : 0, iso-C_16 : 0 and iso-C_17 : 0. The genomic DNA G+C content of strain NEAU-LLB^T was 70.2 mol%. In addition, the average nucleotide identity values between strain NEAU-LLB^T and its reference strains, M. paludicola DSM 16915^T, M. marinilacus DSM 18904^T and M. album SYSU D8007^T, were found to be 81.1, 79.4 and 78.7 %, respectively, and the level of digital DNA-DNA hybridization between them were 23.8, 22.6 and 21.8 %, respectively. Based on the phenotypic, phylogenetic and genotypic data, strain NEAU-LLB^T is considered to represent a novel species of the genus Microbacterium, for which the name Microbacterium stercoris sp. nov is proposed, with NEAU-LLB^T (=CCTCC AA 2018028^T=JCM 32660^T) as the type strain.

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.

From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes

Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.

Microbacterium helvum sp. nov., a novel actinobacterium isolated from cow dung

A Gram-positive, aerobic, non-motile, non-spore-forming, short rod-shaped strain, NEAU-LLC^T, was isolated from cow dung in Shangzhi City, Heilongjiang Province, Northeast China and identified by a polyphasic taxonomic study. Colonies was light yellow, round, with entire margin. Strain NEAU-LLC^T was grown at 15-45 ℃ and pH 6.0-10.0. NaCl concentration ranged from 0 to 5% (W/V). The 16S rRNA gene sequence of NEAU-LLC^T showed the high similarities with Microbacterium kyungheense JCM 18735^T (98.5%), Microbacterium trichothecenolyticum JCM 1358^T (98.3%) and Microbacterium jejuense JCM 18734^T (98.2%). The whole-cell sugars were glucose, rhamnose and ribose. The menaquinones contained MK-12 and MK-13. Ornithine, glutamic acid, lysine and a small amount of alanine and glycine were the amino acids in the hydrolyzed products of the cell wall. The major fatty acids were iso-C_16:0, iso-C_18:0, anteiso-C_15:0 and anteiso-C_17:0. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The genome of NEAU-LLC^T was 4,369,375 bp and G + C content is 70.28 mol%. A combination of DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-LLC^T could be distinguished from its closely related strains. Therefore, the strain NEAU-LLC^T was considered to represent a novel species, which was named Microbacterium helvum sp. (Type strain NEAU-LLC^T = CCTCC AA 2018026^T = JCM 32661^T).

Microbacterium algeriense sp. nov., a novel actinobacterium isolated from Algerian oil production waters

A non-motile, straight-rod-shaped, Gram-stain-positive and facultative anaerobic bacterium (i.e., strain G1^T) was isolated from production waters from an Algerian oilfield. Growth was observed in the presence of 0.3-3.5 % (w/v) NaCl, at 20-50 °C and at pH 6.0-9.0. Results of phylogenetic analyses based on 16S rRNA gene sequences showed that strain G1^T belonged to the genus Microbacterium. Strain G1 ^T was closely related to Microbacterium oxydans (DSM 20578^T) and Microbacterium maritypicum (DSM 12512^T) with 99.8 % sequence similarity and to Microbacterium saperdae (DSM 20169^T) with 99.6 % sequence similarity. Strain G1 ^T contained MK9, MK10, MK11, MK12 and MK13 as respiratory quinones, and phosphatidylglycerol, diphosphatidylglycerol and glycolipid as the major polar lipids. The major cellular fatty acids were anteiso-C_15:0, iso-C_16:0 and anteiso-C_17:0. The estimated DNA G+C content was 69.57 mol% based on its draft genome sequence. Genome annotation of strain G1^T predicted the presence of 3511 genes, of which 3483 were protein-coding and 47 were tRNA genes. The DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) values between strain G1^T and M. oxydans (DSM 20578^T) and M. maritypicum (DSM 12512^T) were in both cases far below the respective species boundary thresholds (27.5 and 28.0 % for DDH; and 84.40 and 84.82% for ANI, respectively). Based on the data presented above, strain G1^T was considered to represent a novel species for which the name Microbacterium algeriense is proposed with the type strain G1^T (=DSM 109018^T=LMG 31276^T).

Antimicrobial and Antioxidant Effects of a Forest Actinobacterium V002 as New Producer of Spectinabilin, Undecylprodigiosin and Metacycloprodigiosin

The aim of the study is the research and identification of a Streptomyces strain as a new producer of spectinabilin, undecylprodigiosin and metacycloprodigiosin. Among 54 actinomycete isolates isolated from El-Ogbane forest soils in Algeria, only one isolate, designated V₀₀₂, was selected for its ability to produce prodigiosins. The selected strain was analysed for its ability to produce three different secondary metabolites as well as their biological activities. V₀₀₂ belongs to the Streptomyces genus and has significant antimicrobial and antioxidant activities. The taxonomic position of V₀₀₂ by 16S rRNA sequence analysis showed a similarity of 99.93% with Streptomyces lasiicapitis DSM 103124^T and 98.96% with Streptomyces spectabilis DSM 40512^T. Fractionation of crude secondary metabolites produced by the strain using HPLC-MS revealed the presence of spectinabilin, undecylprodigiosin and metacycloprodigiosin, which demonstrated significant activity. Strain V₀₀₂ is considered a new producer of spectinabilin, undecylprodigiosin and metacycloprodigiosin with significant antimicrobial and antioxidant activity.

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and CO₂ production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (β-carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment.