Genus Kitasatospora, taxonomic features and diversity of secondary metabolites

The Advancement of Peptides Derived From Kitasatospora

Kitasatospora continue to be a rich source of chemically diverse and bioactive peptide natural products. This review highlights two strategies in peptide natural products research of Kitasatospora: (1) a natural products-first approach guided by a major compound, biological activity, or genomic analysis, and (2) an enzyme-first approach guided by bioinformatic tools to construct a sequence similarity network for the discovery of biosynthetic enzymes. The structures of peptides, biosynthetic origins of unique building blocks, recent reports of post-translational modifying enzymes for constructing these peptides, and knowledge gaps in biosynthesis will also be presented. Actinobacteria belonging to the genus Kitasatospora are a source of biosynthetic enzymes to expand the biocatalytic toolbox for synthetic biology.

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.

Kitasatospora hibisci sp. nov., a novel actinomycete with antimicrobial potential isolated from rhizosphere soil of Hibiscus tiliaceus in Guangxi

A novel Kitasatospora strain, designated as HNM1077T, was isolated from rhizosphere soil of Hibiscus tiliaceus collected from the bank of the Beilun River in Dongxing City, Guangxi Province, China. The novel strain exhibited antimicrobial activity against a wide range of microbes, particularly Gram--negative bacteria and plant pathogenic fungi. Based on the alignment of 16S rRNA gene sequences, strain HNM1077T was closely related to Kitasatospora aburaviensis NRRL B-2218T (99.51%). Comparisons based on genome sequencing showed that strain HNM1077T was distinguished from its nearest species by average nucleotide identity of 94.36% and a digital DNA-DNA hybridization value of 54.3%. The G+C content of strain HNM1077T was 73.1 mol%. The main fatty acids of strain HNM1077T were iso-C15:0 (21.5%), anteiso-C15:0 (11.7%), iso-C16:0 (8.6%), iso-C17:0 (9.3%) and anteiso-C17:0 (8.7%). The predominant menaquinone was MK-9 (H8). The major polar lipids of strain HNM1077T consisted of phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol and glycosylphosphatidylinositol. Based on these polyphasic taxonomic results, strain HNM1077T represents a novel Kitasatospora species, for which the name Kitasatospora hibisci sp. nov. is proposed. The type strain is HNM1077T (=CCTCC AA 2024052T=KCTC 59330T).

Kitasatospora camelliae sp. nov., isolated from rhizosphere soil of Camellia oleifera

Strain HUAS MG31T was isolated from the rhizosphere soil of Camellia oleifera collected from Taoyuan County, China. This strain produced white substrate mycelium and hair brown aerial mycelium without diffusible pigment on the Gause's synthetic No. 1 medium. Aerial mycelia differentiated into rectiflexible spore chains consisting of spherical or cylindrical spores with smooth surfaces. Cell wall peptidoglycan of strain HUAS MG31T contained meso-diaminopimelic acid, and whole-cell sugars were galactose and mannose. The menaquinones of strain HUAS MG31T were MK-9(H6), MK-9(H8) and MK-9(H4). The major cellular fatty acids consisted of Summed Feature 9 (iso-C17 : 1 ω9c/10-methyl C16 : 0), iso-C16 : 0, iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0, Summed Feature 3 (iso H-C16 : 1 /C16 : 1 ω6c) and cyclo C17 : 0. Sequence analysis based on the full-length 16S rRNA gene of strain HUAS MG31T showed that it shared highest sequence similarities to Kitasatospora paranensis HKI 0190T (99.5%) and Kitasatospora terrestris HKI 0186T (99.4%). The phylogenomic tree shows that strain HUAS MG31T forms an independent subclade, indicating that it might belong to a potential novel species. The results from phylogenetic trees based on 16S rRNA gene sequences showed that strain HUAS MG31T was most closely related to K. paranensis HKI 0190T. However, the average nucleotide identity and the digital DNA-DNA hybridization between strain HUAS MG31T and K. paranensis JCM 13005T were 87.0 %/81.2% and 25.8 %, respectively, below the 95%-96% and 70 % threshold that defined a new species. Meanwhile, phenotypic, chemotaxonomic characteristics and MALDI-TOF MS results further confirmed that strain HUAS MG31T was significantly different from K. paranensis JCM 13005T. Therefore, these results reveal that strain HUAS MG31T represents a novel species of the genus Kitasatospora, for which the name Kitasatospora camelliae sp. nov. is proposed. The type strain is HUAS MG31T (=MCCC 1K09225T= JCM 37022T).

Biodiversity and Antifungal Activities of Amazonian Actinomycetes Isolated from Rhizospheres of Inga edulis Plants

BACKGROUND

Actinobacteria are major producers of antibacterial and antifungal metabolites and are growing their search for substances of biotechnological interest, especially for use in agriculture, among other applications. The Amazon is potentially rich in actinobacteria; however, almost no research studies exist. Thus, we present a study of the occurrence and antifungal potential of actinobacteria from the rhizosphere of Inga edulis, a native South American plant and one that is economically useful in the whole of the Amazon.

METHODS

Among the 64 actinobacteria strains isolated from the rhizosphere of three Inga edulis plants, 20 strains were selected and submitted to dual-culture assays against five important phytopathogenic fungi and morphological and 16S rRNA gene analyses. Two strains, LaBMicrA B270 and B280, were also studied for production curves of metabolic extracts and antifungal activities, including their minimum inhibitory concentration (MIC) against phytopathogenic fungi.

RESULTS

Among the 20 strains, 90% were identified as Streptomyces and 10% as Kitasatospora. All the strains showed antagonisms against two or more of five phytopathogens: Corynespora cassiicola, Colletotrichum guaranicola, Colletotrichum sp., Pestalotiopsis sp., and Sclerotium coffeicola. Streptomyces spp. strains LaBMicrA B270 and B280 were active against phytopathogens of the guarana plant (Paullinia cupana). Furthermore, AcOEt/2-propanol 9:1 extract from the 10-day strain LaBMicrA B280 cultured medium presented activity against all the phytopathogens tested, with a minimum inhibitory concentration of 125 μg/mL.

CONCLUSIONS

The results revealed various actinomycetes in three rhizospheres of I. edulis in the Amazon and the high potential of metabolic extracts from some of these bacterial strains against phytopathogenic fungi that destroy numerous crops.

The Secondary Metabolites from Genus Kitasatospora: A Promising Source for Drug Discovery

Microbial secondary metabolites are well-known resource for drug discovery. Kitasatospora is one of the rare genera of Actinomycetes and important antibiotics producer that are not fully explored. Recently an explosively increasing number of reports have proved that the genus is capable of producing various bioactive secondary metabolites. Here, we comprehensively summarized secondary metabolites from Kitasatospora strains including their chemical structures, biological effects, mechanisms of actions together with the related genomic and biosynthetic analyses. The review covered more than 100 metabolites with their significant pharmacological properties. Some of these natural products which include tyropeptin has been optimized to a promising lead compound. This work provides detailed information of Kitasatospora-derived natural products and presents their potential for therapeutically relevant utilization, which would inspire the drug discovery from this genus in future.

"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems"

Geosmin and 2-methylisoborneol (MIB) are known to cause taste-and-odour problems in recirculating aquaculture systems (RAS). Both geosmin and MIB are microbial metabolites belonging to terpenoids. Precursors for terpenoids are biosynthesized via the methylerythritol phosphate (MEP) and the mevalonate (MVA) pathways. We carried out a metagenomic analysis of 50 samples from five RAS to investigate terpenoid biosynthesis and metabolic potential for geosmin and MIB production in RAS microbiomes. A total of 1008 metagenome-assembled genomes (MAGs) representing 26 bacterial and three archaeal phyla were recovered. Although most archaea are thought to use the MVA pathway for terpenoid precursor biosynthesis, an Iainarchaeota archaeal MAG is shown to harbour a complete set of genes encoding the MEP pathway but lacking genes associated with the MVA pathway. In this study, a total of 16 MAGs affiliated with five bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexota, and Myxococcota) were identified as possessing potential geosmin or MIB synthases. These putative taste and odour producers were diverse, many were taxonomically unidentified at the genus or species level, and their relative abundance differed between the investigated RAS farms. The metagenomic study of the RAS microbiomes revealed a previously unknown phylogenetic diversity of the potential to produce geosmin and MIB.

Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

The biotechnological industry faces a crucial demand for novel bioactive compounds, particularly antimicrobial agents, to address the rising challenge of bacterial resistance to current available antibiotics. Traditional strategies for cultivating naturally occurring microorganisms often limit the discovery of novel antimicrobial producers. This study presents a protocol for targeted selection of bacterial strains using the supernatant of Paenibacillus elgii, which produces abundant signal molecules and antimicrobial peptides. Soil samples were inoculated in these enriched culture media to selectively cultivate bacteria resistant to the supernatant, indicating their potential to produce similar compounds. The bacterial strains isolated through this method were assessed for their antibacterial activity. In addition, the functional annotation of the genome of one of these strains revealed several gene clusters of biotechnological interest. This study highlights the effectiveness of using this approach for selective cultivation of microorganisms with potential for biotechnological applications.

Amazonian Bacteria from River Sediments as a Biocontrol Solution against Ralstonia solanacearum

Bacterial wilt, caused by Ralstonia solanacearum, is one of the main challenges for sustainable tomato production in the Amazon region. This study evaluated the potential of bacteria isolated from sediments of the Solimões and Negro rivers for the biocontrol of this disease. From 36 bacteria selected through in vitro antibiosis, three promising isolates were identified: Priestia aryabhattai RN 11, Streptomyces sp. RN 24, and Kitasatospora sp. SOL 195, which inhibited the growth of the phytopathogen by 100%, 87.62%, and 100%, respectively. These isolates also demonstrated the ability to produce extracellular enzymes and plant growth-promoting compounds, such as indole-3-acetic acid (IAA), siderophore, and ammonia. In plant assays, during both dry and rainy seasons, P. aryabhattai RN 11 reduced disease incidence by 40% and 90%, respectively, while promoting the growth of infected plants. Streptomyces sp. RN 24 and Kitasatospora sp. SOL 195 exhibited high survival rates (85-90%) and pathogen suppression in the soil (>90%), demonstrating their potential as biocontrol agents. This study highlights the potential of Amazonian bacteria as biocontrol agents against bacterial wilt, contributing to the development of sustainable management strategies for this important disease.

Genomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil

An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).

Biotechnological potential of actinomycetes in the 21st century: a brief review

This brief review aims to draw attention to the biotechnological potential of actinomycetes. Their main uses as sources of antibiotics and in agriculture would be enough not to neglect them; however, as we will see, their biotechnological application is much broader. Far from intending to exhaust this issue, we present a short survey of the research involving actinomycetes and their applications published in the last 23 years. We highlight a perspective for the discovery of new active ingredients or new applications for the known metabolites of these microorganisms that, for approximately 80 years, since the discovery of streptomycin, have been the main source of antibiotics. Based on the collected data, we organize the text to show how the cosmopolitanism of actinomycetes and the evolutionary biotic and abiotic ecological relationships of actinomycetes translate into the expression of metabolites in the environment and the richness of biosynthetic gene clusters, many of which remain silenced in traditional laboratory cultures. We also present the main strategies used in the twenty-first century to promote the expression of these silenced genes and obtain new secondary metabolites from known or new strains. Many of these metabolites have biological activities relevant to medicine, agriculture, and biotechnology industries, including candidates for new drugs or drug models against infectious and non-infectious diseases. Below, we present significant examples of the antimicrobial spectrum of actinomycetes, which is the most commonly investigated and best known, as well as their non-antimicrobial spectrum, which is becoming better known and increasingly explored.

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

The actinomycete Kitasatospora sp. SeTe27, subjected to adaptive laboratory evolution (ALE) in the presence of selenite, varies its cellular morphology, redox stability, and tolerance to the toxic oxyanion

The effects of oxyanions selenite (SeO32-) in soils are of high concern in ecotoxicology and microbiology as they can react with mineral particles and microorganisms. This study investigated the evolution of the actinomycete Kitasatospora sp. SeTe27 in response to selenite. To this aim, we used the Adaptive Laboratory Evolution (ALE) technique, an experimental approach that mimics natural evolution and enhances microbial fitness for specific growth conditions. The original strain (wild type; WT) isolated from uncontaminated soil gave us a unique model system as it has never encountered the oxidative damage generated by the prooxidant nature of selenite. The WT strain exhibited a good basal level of selenite tolerance, although its growth and oxyanion removal capacity were limited compared to other environmental isolates. Based on these premises, the WT and the ALE strains, the latter isolated at the end of the laboratory evolution procedure, were compared. While both bacterial strains had similar fatty acid profiles, only WT cells exhibited hyphae aggregation and extensively produced membrane-like vesicles when grown in the presence of selenite (challenged conditions). Conversely, ALE selenite-grown cells showed morphological adaptation responses similar to the WT strain under unchallenged conditions, demonstrating the ALE strain improved resilience against selenite toxicity. Whole-genome sequencing revealed specific missense mutations in genes associated with anion transport and primary and secondary metabolisms in the ALE variant. These results were interpreted to show that some energy-demanding processes are attenuated in the ALE strain, prioritizing selenite bioprocessing to guarantee cell survival in the presence of selenite. The present study indicates some crucial points for adapting Kitasatospora sp. SeTe27 to selenite oxidative stress to best deal with selenium pollution. Moreover, the importance of exploring non-conventional bacterial genera, like Kitasatospora, for biotechnological applications is emphasized.

Soil warming increases the number of growing bacterial taxa but not their growth rates

Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.

Genome-based reclassification of Kitasatospora niigatensis as a later heterotypic synonym of Kitasatospora cineracea Tajima et al. (2001)

The present study used genome-based approaches to investigate the taxonomic relationship between Kitasatospora cineracea DSM 44780T and Kitasatospora niigatensis DSM 44781T, two species that were previously described by Tajima et al. (Int J Syst Evol Microbiol 51:1765-1771, 2001). The digital DNA-DNA hybridization (dDDH), average amino acid identity (AAI), and average nucleotide identity (ANI) values between the genomes of the two type strains were 90.3, 98.7, and 99.1%, respectively. These values exceeded the established thresholds of 70% (dDDH) and 95-96% (ANI and AAI) for bacterial species delineation, suggesting that K. cineracea and K. niigatensis should share the same taxonomic position. Furthermore, our analysis using the 'Bacterial Pan Genome Analysis' (BPGA) pipeline and the Maximum Likelihood core-genes tree inferred using FastTree2 consistently demonstrated that K. cineracea DSM 44780T and K. niigatensis DSM 44781T are closely related, as indicated by the clustering of these strains in the core-genes phylogenomic tree. Based on these findings, we propose that K. niigatensis should be considered a later heterotypic synonym of K. cineracea.

Genome sequence and characterization of Streptomyces phages Vanseggelen and Verabelle, representing two new species within the genus Camvirus

Despite the rising interest in bacteriophages, little is known about their infection cycle and lifestyle in a multicellular host. Even in the model system Streptomyces, only a small number of phages have been sequenced and well characterized so far. Here, we report the complete characterization and genome sequences of Streptomyces phages Vanseggelen and Verabelle isolated using Streptomyces coelicolor as a host. A wide range of Streptomyces strains could be infected by both phages, but neither of the two phages was able to infect members of the closely related sister genus Kitasatospora. The phages Vanseggelen and Verabelle have a double-stranded DNA genome with lengths of 48,720 and 48,126 bp, respectively. Both phage genomes contain 72 putative genes, and the presence of an integrase encoding protein indicates a lysogenic lifestyle. Characterization of the phages revealed their stability over a wide range of temperatures (30-45 °C) and pH values (4-10). In conclusion, Streptomyces phage Vanseggelen and Streptomyces phage Verabelle are newly isolated phages that can be classified as new species in the genus Camvirus, within the subfamily Arquattrovirinae.

Kitasatospora fiedleri sp. nov., a novel antibiotic-producing member of the genus Kitasatospora

Strain TÜ4103T was originally sampled from Java, Indonesia and deposited in the Tübingen strain collection under the name 'Streptomyces sp.'. The strain was found to be an antibiotic producer as strain TÜ4103T showed bioactivity against Gram-positive bacteria, such as Bacillus subtilis and Kocuria rhizophila in bioassays. Strain TÜ4103T showed 16S rRNA gene sequence similarity of 99.65 % to Kitasatospora cheerisanensis DSM 101999T and 98.82 % to Kitasatospora niigatensis DSM 44781T and Kitasatospora cineracea DSM 44780T. Genome-based phylogenetic analysis revealed that strain TÜ4103T is closely related to K. cineracea DSM 44780T and K. niigatensis DSM 44781T. The digital DNA-DNA hybridization values between the genome sequences of strain TÜ4103T and its closest phylogenomic relatives, strains DSM 44780T and DSM 44781T, were 43.0 and 42.9 %, respectively. Average nucleotide identity (ANI) values support this claim, with the highest ANI score of 91.14 % between TÜ4103T and K. niigatensis being closely followed by an ANI value of 91.10 % between K. cineracea and TÜ4103T. The genome of TÜ4103T has a size of 7.91 Mb with a G+C content of 74.05 mol%. Whole-cell hydrolysates of strain TÜ4103T are rich in meso-diaminopimelic acid, and rhamnose, galactose and mannose are characteristic as whole-cell sugars. The phospholipid profile contains phosphatidylethanolamine, diphosphatidylglycerol and glycophospholipid. The predominant menaquinones (>93.5 %) are MK-9(H8) and MK-9(H6). Based on the phenotypic, genotypic and genomic characteristics, strain TÜ4103T (=DSM 114396T=CECT 30712T) merits recognition as the type strain of a novel species of the genus Kitasatospora, for which the name Kitasatospora fiedleri sp. nov. is proposed.

Effect of fermented dandelion on productive performance, meat quality, immune function, and intestinal microbiota of broiler chickens

BACKGROUND

Dandelion has a great potential to be used as feed additive. Using microbial fermentation technology to degrade cell walls is conducive to enable better release of bioactive compounds of dandelion. This study intended to explore the effect of fermented dandelion (FD) on production performance, meat quality, immune function, and intestinal microbiota of broiler chickens. One-hundred and twenty 1-day-old male Arbor Acres broiler chickens were randomly allotted into three treatments: CON (basal diet, control), LFD and HFD (basal diet with 500 and 1000 mg/kg FD, respectively), with five replicates of eight birds each. The experiment lasted for 42 days.

RESULTS

The results showed that birds in HFD group had increased ADG during 1-21 days (P < 0.05). On day 21, the bursa of Fabricius index of birds in LFD group was higher (P < 0.05), while the serum contents of IFN-γ and TNF-ɑ were lower in HFD group (P < 0.05). FD supplementation decreased the observed_species, shannon, chao1 and ace indexes (P < 0.05) as well as the abundance of Bacteroidota, Bacteroides, and Alistipes (P < 0.05). Birds in HFD group had higher abundance of Firmicutes and lower abundance of Verrucomicrobiota (P < 0.05). LFD group had lower abundance of unidentified_bacteria (P < 0.05). On day 42, the abdominal fat yield of HFD group was decreased (P < 0.05). Birds in LFD group had lower L* and b* values of breast muscle (P < 0.05), while higher spleen index. The CAT activities of breast muscle of FD groups were higher (P < 0.05).

CONCLUSION

In summary, dietary FD supplementation at 1000 mg/kg improved production performance and immune function and modulated microbiota composition in ileum of broiler chickens. FD can be supplemented in the diet to enhance performance and health of broiler chickens, of which 1000 mg/kg FD is more effective.

Endophytic actinobacteria from wild medicinal plants are a natural source of insecticide to control the African cotton leafworm (Spodoptera littoralis)

Insecticide resistance in agricultural pests has prompted the need to discover novel compounds with new modes of action. We investigated the potency of secondary metabolites from seventy endophytic actinobacteria against laboratory and field strains of Spodoptera littoralis (fourth instar), comparable to the bioinsecticide spinetoram (Radiant SC 12%). Endophytes from Artemisia herba-alba and A. judaica were highly effective. Chemical profiling of the most potent metabolite of the strain Streptomyces sp. ES2 was investigated using LC-QTOF-MS-MS technique, and the activity was validated through molecular docking studies. Metabolic extracts from actinobacteria belonging to Streptomyces, Nocardioides, and Pseudonocardia showed immediate and latent death to the Spodoptera littoralis fourth instar larvae. The metabolite from strain ES2 has shown the most promising and significant histopathological and inhibitory effects on the fourth instar larvae. ES2 metabolite caused lesions in the body wall cuticle, indicating a different mode of action than that of Radiant. Chemical profiling of ES2 showed the presence of cyromazine (molt inhibitor), 4-nitrophenol, and diazinon as key constituents. In conclusion, these findings suggest that secondary metabolites from endophytic actinobacteria inhabiting wild medicinal plants can be a sustainable source for promising natural biocontrol agents. This is the first illustration of the insecticidal activity of Artemisia spp. microbiome, and natural cyromazine synthesis by actinobacteria.

Secondary Metabolic Potential of Kutzneria

Kutzneria is a rare genus of Actinobacteria that harbors a variety of secondary metabolite gene clusters and produces several interesting types of bioactive secondary metabolites. Recent efforts have partially elucidated the biosynthetic pathways of some of these bioactive natural products, suggesting the diversity and specificity of secondary metabolism within this genus. Here, we summarized the chemical structures, biosynthetic pathways, and key metabolic enzymes of the secondary metabolites isolated from Kutzneria strains. In-depth comparative genomic analysis of all six available high-quality Kutzneria genomes revealed that the majority (77%) of the biosynthetic gene cluster families of Kutzneria were untapped and identified homologues of key metabolic enzymes in the putative gene clusters, including cytochrome P450s, halogenases, and flavin-dependent N-hydroxylases. The present study suggests that Kutzneria exhibits great potential to synthesize novel secondary metabolites, encodes a variety of valuable metabolic enzymes, and also provides valuable information for the targeted discovery and biosynthesis of novel natural products from Kutzneria.

Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor

Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.

Generation of a high quality library of bioactive filamentous actinomycetes from extreme biomes using a culture-based bioprospecting strategy

Introduction

Filamentous actinomycetes, notably members of the genus Streptomyces, remain a rich source of new specialized metabolites, especially antibiotics. In addition, they are also a valuable source of anticancer and biocontrol agents, biofertilizers, enzymes, immunosuppressive drugs and other biologically active compounds. The new natural products needed for such purposes are now being sought from extreme habitats where harsh environmental conditions select for novel strains with distinctive features, notably an ability to produce specialized metabolites of biotechnological value.

Methods

A culture-based bioprospecting strategy was used to isolate and screen filamentous actinomycetes from three poorly studied extreme biomes. Actinomycetes representing different colony types growing on selective media inoculated with environmental suspensions prepared from high-altitude, hyper-arid Atacama Desert soils, a saline soil from India and from a Polish pine forest soil were assigned to taxonomically predictive groups based on characteristic pigments formed on oatmeal agar. One hundred and fifteen representatives of the colour-groups were identified based on 16S rRNA gene sequences to determine whether they belonged to validly named or to putatively novel species. The antimicrobial activity of these isolates was determined using a standard plate assay. They were also tested for their capacity to produce hydrolytic enzymes and compounds known to promote plant growth while representative strains from the pine forest sites were examined to determine their ability to inhibit the growth of fungal and oomycete plant pathogens.

Results

Comparative 16S rRNA gene sequencing analyses on isolates representing the colour-groups and their immediate phylogenetic neighbours showed that most belonged to either rare or novel species that belong to twelve genera. Representative isolates from the three extreme biomes showed different patterns of taxonomic diversity and characteristic bioactivity profiles. Many of the isolates produced bioactive compounds that inhibited the growth of one or more strains from a panel of nine wild strains in standard antimicrobial assays and are known to promote plant growth. Actinomycetes from the litter and mineral horizons of the pine forest, including acidotolerant and acidophilic strains belonging to the genera Actinacidiphila, Streptacidiphilus and Streptomyces, showed a remarkable ability to inhibit the growth of diverse fungal and oomycete plant pathogens.

Discussion

It can be concluded that selective isolation and characterization of dereplicated filamentous actinomyctes from several extreme biomes is a practical way of generating high quality actinomycete strain libraries for agricultural, industrial and medical biotechnology.

Dietary Epimedium extract supplementation improves intestinal functions and alters gut microbiota in broilers

BACKGROUND

Growth-promoting antibiotics have been banned by law in the livestock and poultry breeding industry in many countries. Various alternatives to antibiotics have been investigated for using in livestock. Epimedium (EM) is an herb rich in flavonoids that has many beneficial effects on animals. Therefore, this study was planned to explore the potential of EM as a new alternative antibiotic product in animal feed.

METHODS

A total of 720 1-day-old male broilers (Arbor Acres Plus) were randomly divided into six groups and fed basal diet (normal control; NC), basal diet supplemented with antibiotic (75 mg/kg chlortetracycline; CTC), and basal diet supplemented with 100, 200, 400 or 800 mg/kg EM extract for 6 weeks (EM100, EM200, EM400 and EM800 groups). The growth performance at weeks 3 and 6 was measured. Serum, intestinal tissue and feces were collected to assay for antioxidant indexes, intestinal permeability, lactic acid and short-chain fatty acids (SCFAs) profiles, microbial composition, and expression of intestinal barrier genes.

RESULTS

The average daily feed intake in CTC group at 1-21 d was significantly higher than that in the NC group, and had no statistical difference with EM groups. Compared with NC group, average daily gain in CTC and EM200 groups increased significantly at 1-21 and 1-42 d. Compared with NC group, EM200 and EM400 groups had significantly decreased levels of lipopolysaccharide and D-lactic acid in serum throughout the study. The concentrations of lactic acid, acetic acid, propionic acid, butyric acid and SCFAs in feces of birds fed 200 mg/kg EM diet were significantly higher than those fed chlortetracycline. The dietary supplementation of chlortetracycline and 200 mg/kg EM significantly increased ileal expression of SOD1, Claudin-1 and ZO-1 genes. Dietary supplemented with 200 mg/kg EM increased the relative abundances of g_NK4A214_group and Lactobacillus in the jejunal, while the relative abundances of Microbacterium, Kitasatospora, Bacteroides in the jejunal and Gallibacterium in the ileum decreased.

CONCLUSION

Supplementation with 200 mg/kg EM extract improved the composition of intestinal microbiota by regulating the core bacterial genus Lactobacillus, and increased the concentration of beneficial metabolites lactic acid and SCFAs in the flora, thereby improving the antioxidant capacity and intestinal permeability, enhancing the function of tight junction proteins. These beneficial effects improved the growth performance of broilers.

Kitasatospora humi sp. nov., isolated from a tropical peat swamp forest soil, and proposal for the reclassification of Kitasatospora psammotica as a later heterotypic synonym of Kitasatospora aureofaciens

A polyphasic approach was used to describe strain RB6PN24T, a novel actinobacterium isolated from peat swamp forest soil collected from Rayong province, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Kitasatospora and showed the highest sequence similarities to Kitasatospora kifunensis IFO 15206T (98.7 %) and Kitasatospora acidiphila MMS16-CNU292T (98.5 %). Strain RB6PN24T contained major amounts of meso-diaminopimelic acid, galactose, mannose and ribose in the whole-cell hydrolysates. MK-9(H6) and MK-9(H8) were the predominant menaquinones of the micro-organism. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, an unidentified lipid, four unidentified aminolipids and six unidentified phospholipids. Mycolic acids were not present. The major fatty acids were iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0, iso-C17:0, anteiso-C17 : 0 and C16 : 0. The draft genome size of strain RB6PN24T was 8.09 Mbp, with 72.1 mol% G+C content and predicted to contain at least 44 biosynthetic gene clusters encoding diverse secondary metabolites. Furthermore, the strain exhibited low average nucleotide identity and digital DNA–DNA hybridization values with K. acidiphila MMS16-CNU292T (89.1 %, 42.4 %) and K. kifunensis DSM 41654T (79.5 %, 25.5 %). The results of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses revealed that strain RB6PN24T represents a novel species of the genus Kitasatospora , for which the name Kitasatospora humi sp. nov. is proposed. The type strain is RB6PN24T (=TBRC 14818T=NBRC 115116T). In addition, the comparison of the whole genome sequences and phenotypic features suggested that Kitasatospora aureofaciens and Kitasatospora psammotica belong to the same species. Therefore, it is proposed that K. psammotica is reclassified as a later heterotypic synonym of K. aureofaciens .

Chemically Protected Sodium Butyrate Improves Growth Performance and Early Development and Function of Small Intestine in Broilers as One Effective Substitute for Antibiotics

The purpose of this study was to investigate the effects of chemically protected sodium butyrate (CSB) on growth performance and the early development and function of small intestine in broilers as one potential substitute for antibiotics. A total of 192 one-day-old Arbor Acres male broilers were randomly assigned into three dietary treatment groups (eight replicates per treatment): the control (CON) diet; ANT diet, CON diet supplemented with the antibiotics (enramycin, 8 mg/kg and aureomycin, 100 mg/kg); CSB diet, CON diet supplemented with 1000 mg/kg CSB, respectively. The results showed that dietary CSB and antibiotics addition significantly improved the growth performance of broilers by increasing the body weight gain (BWG) and feed conversion ratio (FCR) during different stages (p < 0.05). On day 21, the supplement of CSB in diet improved the structure of small intestine (duodenum, jejunum, and ileum) in broilers by increasing the ratio of villus height to crypt depth (VH/CD) (p < 0.05) and enhanced the butyric acid (BA) (p < 0.05) and total short chain fatty acids (SCFA) concentrations of small intestine (jejunum and ileum) compared with the CON and ANT diets. Besides that, the superoxide dismutase (SOD), total antioxidant capacity (TAC) and TAC to malondialdehyde (TAC/MDA) ratio of the ileal and jejunal mucosa were significantly higher (p < 0.05) in the CSB and ANT than in the CON. In addition, the supplement of CSB in diet markedly significantly enhanced α-amylase, lipase, and trypsin activities of the ileum (p < 0.05) as compared to the ANT diet. 16S rRNA gene sequencing indicated that CSB markedly increased the microbiota diversity of ileum in broilers at 21 days of age as compared to CON and ANT (p < 0.05). Furthermore, we found that Firmicutes was the predominant phyla and Lactobacillus was the major genus in the ileum of broilers. Compared with the ANT diet, the supplement of CSB in diet increased the relative abundance of some genera microbiota (e.g., Candidatus_Arthromitus, Romboutsia) by decreasing the relative abundance of Lactobacillus. Moreover, Akkermansia in the CSB was the highest in comparison to that in the CON and ANT. In addition, Kitasatospora that belongs to the phylum Actinobacteriota was only found in ileum of broilers fed the ANT diet. In summary, the supplement of 1000 mg/kg CSB in the diet improved the growth performance by promoting early development and function of the small intestine, which is associated with the regulation of intestinal flora and reestablishment of micro-ecological balance in broilers. Thus, CSB has great potential value as one of effective substitutes for in-feed antibiotics in the broiler industry.

Adaptation to Endophytic Lifestyle Through Genome Reduction by Kitasatospora sp. SUK42

Endophytic actinobacteria offer great potential as a source of novel bioactive compounds. In order to investigate the potential for the production of secondary metabolites by endophytes, we recovered a filamentous microorgansism from the tree Antidesma neurocarpum Miq. After phenotypic analysis and whole genome sequencing we demonstrated that this organism, SUK42 was a member of the actinobacterial genus Kitasatospora. This strain has a small genome in comparison with other type strains of this genus and has lost metabolic pathways associated with Stress Response, Nitrogen Metabolism and Secondary Metabolism. Despite this SUK42 can grow well in a laboratory environment and encodes a core genome that is consistent with other members of the genus. Finally, in contrast to other members of Kitasatospora, SUK42 encodes saccharide secondary metabolite biosynthetic gene clusters, one of which with similarity to the acarviostatin cluster, the product of which displays α-amylase inhibitory activity. As extracts of the host plant demonstrate this inhibitory activity, it suggests that the potential medicinal properties of A. neurocarpum Miq might be provided by the endophytic partner and illustrate the potential for exploitation of endophytes for clinical or industrial uses.

Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to Streptomyces

While the genus Streptomyces (family Streptomycetaceae) has been studied as a model for bacterial secondary metabolism and genetics, its close relatives have been less studied. The genus Kitasatospora is the second largest genus in the family Streptomycetaceae. However, its taxonomic position within the family remains under debate and the secondary metabolic potential remains largely unclear. Here, we performed systematic comparative genomic and phylogenomic analyses of Kitasatospora. Firstly, the three genera within the family Streptomycetaceae (Kitasatospora, Streptomyces, and Streptacidiphilus) showed common genomic features, including high G + C contents, high secondary metabolic potentials, and high recombination frequencies. Secondly, phylogenomic and comparative genomic analyses revealed phylogenetic distinctions and genome content differences among these three genera, supporting Kitasatospora as a separate genus within the family. Lastly, the pan-genome analysis revealed extensive genetic diversity within the genus Kitasatospora, while functional annotation and genome content comparison suggested genomic differentiation among lineages. This study provided new insights into genomic characteristics of the genus Kitasatospora, and also uncovered its previously underestimated and complex secondary metabolism.

Microbial communities in rare earth mining soil after in-situ leaching mining

In-situ leaching technology is now widely used to exploit ion adsorption rare earth ore, which has caused serious environmental problems and deterioration of mining soil ecosystems. However, our knowledge about the influences of mining operation on the microbiota in these ecosystems is currently very limited. In this study, diversity and composition of prokaryote and ammonia-oxidizing microorganisms in rare earth mining soil after in-situ leaching practice were examined using quantitative Polymerase Chain Reaction (qPCR) and Illumina high-throughput sequencing. Results showed that in-situ leaching mining considerably impacted microbial communities of the mining soils. The abundances of bacterial, archaeal, and ammonia-oxidizing archaea (AOA) were significantly and negatively correlated with ionic rare earth elements (REEs), while their diversities were relatively stable. Total rare earth elements (TREEs) and ammonium were the strongest predictors of the bacterial community structure, and organic matter was the key factor predicting the variation in the archaeal community. Chloroflexi, Proteobacteria, Acidobacteria, and Actinobacteria were the most abundant bacterial phyla, and archaeal communities were dominated by Thaumarchaeota. Phylogenetic analysis indicated that unclassified Thaumarchaeota and Crenarchaeota were the predominant AOA groups. The non-detection of ammonia-oxidizing bacteria (AOB) and the abundance of AOA indicated that archaea rather than bacteria were predominantly responsible for ammonia oxidation in the mining soil. Network analysis demonstrated that positive interactions among microorganisms could increase their adaptability or resistance to this harsh environment. This study provides a comprehensive analysis of the prokaryotic communities and functional groups in rare earth mining soil after mining operation, as well as insight into the potential interactive mechanisms among soil microbes.

Genome Mining of the Genus Streptacidiphilus for Biosynthetic and Biodegradation Potential

The genus Streptacidiphilus represents a group of acidophilic actinobacteria within the family Streptomycetaceae, and currently encompasses 15 validly named species, which include five recent additions within the last two years. Considering the potential of the related genera within the family, namely Streptomyces and Kitasatospora, these relatively new members of the family can also be a promising source for novel secondary metabolites. At present, 15 genome data for 11 species from this genus are available, which can provide valuable information on their biology including the potential for metabolite production as well as enzymatic activities in comparison to the neighboring taxa. In this study, the genome sequences of 11 Streptacidiphilus species were subjected to the comparative analysis together with selected Streptomyces and Kitasatospora genomes. This study represents the first comprehensive comparative genomic analysis of the genus Streptacidiphilus. The results indicate that the genomes of Streptacidiphilus contained various secondary metabolite (SM) producing biosynthetic gene clusters (BGCs), some of them exclusively identified in Streptacidiphilus only. Several of these clusters may potentially code for SMs that may have a broad range of bioactivities, such as antibacterial, antifungal, antimalarial and antitumor activities. The biodegradation capabilities of Streptacidiphilus were also explored by investigating the hydrolytic enzymes for complex carbohydrates. Although all genomes were enriched with carbohydrate-active enzymes (CAZymes), their numbers in the genomes of some strains such as Streptacidiphilus carbonis NBRC 100919^T were higher as compared to well-known carbohydrate degrading organisms. These distinctive features of each Streptacidiphilus species make them interesting candidates for future studies with respect to their potential for SM production and enzymatic activities.

Kitasatospora acidiphila sp. nov., isolated from pine grove soil, exhibiting antimicrobial potential

A polyphasic study was carried out to establish the taxonomic position of an acidophilic isolate designated MMS16-CNU292T (=JCM 32302T) from pine grove soil, and provisionally assigned to the genus Kitasatospora . On the basis of 16S rRNA gene sequence similarity, the strain formed a novel evolutionary lineage within Kitasatospora and showed highest similarities to Kitasatospora azatica KCTC 9699T (98.75 %), Kitasatospora kifunensis IFO 15206T (98.74 %), Kitasatospora purpeofusca NRRL B-1817T (98.61 %) and Kitasatospora nipponensis HKI 0315T (98.42 %), respectively. Strain MMS16-CNU292T possessed MK-9(H6) and MK-9(H8) as the major menaquinones, and a major amount of meso-diaminopimelic acid in the cell-wall peptidoglycan. The whole-cell hydrolysates were rich in galactose, glucose and mannose, and the polar lipids mainly consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylglycerol and phosphatidylinositol mannosides. The major fatty acids were anteiso-C15 : 1-A, anteiso-C15 : 0, and iso-C15 : 0, and the DNA G+C content was 71.5 mol%. The strain exhibited antibacterial activity against a number of bacterial strains, and the activity was generally greater when grown in acidic conditions. The phylogenetic, chemotaxonomic and phenotypic properties enabled distinction of MMS16-CNU292T from related species, and thus the isolate should be recognized as a new species of the genus Kitasatospora , for which the name Kitasatospora acidiphila sp. nov. (type strain=MMS16-CNU292T=KCTC 49011T=JCM 32302T) is proposed.

Nonocarbolines A-E, β-Carboline Antibiotics Produced by the Rare Actinobacterium Nonomuraea sp. from Indonesia

During the course of our ongoing screening for novel biologically active secondary metabolites, the rare Actinobacterium, Nonomuraea sp. 1808210CR was found to produce five unprecedented β-carboline derivatives, nonocarbolines A-E (1-5). Their structures were elucidated from high-resolution mass spectrometry, 1D and 2D nuclear magnetic resonance spectroscopy, and the absolute configuration of 4 was determined by using the modified Mosher method. Nonocarboline B (2) displayed moderate antifungal activity against Mucor hiemalis, while nonocarboline D (4) exhibited significant cytotoxic activity against the human lung carcinoma cell line A-549 with the IC50 value of 1.7 µM.

Genome based characterization of Kitasatospora sp. MMS16-BH015, a multiple heavy metal resistant soil actinobacterium with high antimicrobial potential

An actinobacterial strain designated Kitasatospora sp. MMS16-BH015, exhibiting high level of heavy metal resistance, was isolated from soil of an abandoned metal mining site, and its potential for metal resistance and secondary metabolite production was studied. The strain was resistant to multiple heavy metals including zinc (up to 100 mM), nickel (up to 2 mM) and copper (up to 0.8 mM), and also showed antimicrobial potential against a broad group of microorganisms, in particular filamentous fungi. The genome of strain MMS16-BH015 was 8.96 Mbp in size with a G + C content of 72.7%, and contained 7270 protein-coding genes and 107 tRNA/rRNA genes. The genome analysis revealed presence of at least 121 metal resistance related genes, which was prominently higher in strain MMS16-BH015 compared to other genomes of Kitasatospora. The genes included those for proteins representing various families involved in the transport of heavy metals, for example dipeptide transport ATP-binding proteins, high-affinity nickel transport proteins, and P-type heavy metal-transporting ATPases. Additionally, 43 biosynthetic gene clusters (BGCs) for secondary metabolites, enriched with those for non-ribosomal peptides, were detected in this multiple heavy metal resistant actinobacterium, which was again the highest among the compared genomes of Kitasatospora. The pan-genome analysis also identified higher numbers of unique genes related to secondary metabolite production and metal resistance mechanism in strain MMS16-BH015. A high level of correlation between the biosynthetic potential and heavy metal resistance could be observed, thus indicating that heavy metal resistant actinobacteria can be a promising source of bioactive compounds.

Paraconexibacter algicola gen. nov., sp. nov., a novel actinobacterium isolated from a eutrophic lake during the end of cyanobacterial harmful algal blooms, and proposal of Paraconexibacteraceae fam. nov. in the order Solirubrobacterales

A novel bacterium, strain Seoho-28^T, was isolated from a shallow eutrophic lake during the end of cyanobacterial harmful algal blooms and was characterized taxonomically and phylogenetically. Strain Seoho-28^T was a Gram-stain-negative, aerobic, rod-shaped and non-motile bacterium. The strain grew optimally with 0 % NaCl and at 25-30 °C on Reasoner's 2A medium. The phylogenetic analysis based on 16S rRNA gene sequences positioned the novel strain among the order Solirubrobacterales, but sequence similarities to known species were less than 94.7 %. The genomic DNA G+C content of the strain Seoho-28^T was 74.2 mol%. Genomic comparisons of strain Seoho-28^T with families in the order Solirubrobacterales were made using the Genome-to-Genome Distance Calculator, average nucleotide identity and average amino acid identity analyses (values indicated ≤14.9, ≤73.5 and ≤57.8 %, respectively). Strain Seoho-28^T contained C_16 : 0-iso, C_18 : 1  ω9c and C_16 : 0 as major fatty acids and MK-7 (H₄) as the major quinone. Strain Seoho-28^T contained diphosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid as major polar lipids. Meso- and ll-diaminopimelic acids were the diagnostic diamino acids in the cell-wall peptidoglycan. Based on the genotypic, chemotaxonomic and phenotypic results, strain Seoho-28^T represents a novel genus and species, Paraconexibacter algicola gen. nov., sp. nov., which belongs to a new family Paraconexibacteraceae in the order Solirubrobacterales and the class Thermoleophilia. The type strain is Seoho-28^T (=KCTC 39791^T=JCM 31881^T).

Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum

The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that Leontopodium nivale subsp. alpinum (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pre-treatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera Actinokineospora, Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus, Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.

An integrated bioaugmentation/electrocoagulation concept for olive mill wastewater management and the reuse in irrigation of biofuel plants: a pilot study

A consortium of highly degrading microorganisms was used in an integrated bioaugmentation/electrocoagulation process for treating olive mill wastewater. The system was investigated for treating 1 m³ day^-1, at a pilot scale, for 2 years; hydraulic loading rate and organic loading rate were 2880 l m^-2 day^-1 and 37,930 g COD m^-2 day^-1, respectively. Average removal efficiency for COD, oils, and total phenols was 63.9%, 85.2%, and 43.6%, respectively. The olive mill consortium, OMC, consisted of seven actinomycete strains. The strains were confirmed, by 16S rDNA analysis, to belong to five Streptomyces, one Kitasatospora, and one Micromonospora strains, at 100-99.06% similarities. Hydrolytic enzyme activities of OMC strains were remarkably higher for degrading cellulosic and lipid constituents (enzyme-cumulative indices, 14-16.1), than the phenolic constituents (indices, 4.1-6.5). The establishment of actinomycetes in the treatment system was indicated by their increased counts in the biofilm at the end of the biofilter, reaching 13-fold higher than that in the control bed. The treated effluent was toxic to the seedlings of Jatropha curcas (Jatropha) and Simmondsia chinensis (Jojoba). Though its application in irrigation of 3-year-old Jatropha shrubs, significantly, enhanced the fruit yield up to 1.85-fold higher than the control, without affecting the seed oil content, after 3-month application, the irrigated soil showed insignificant changes in its biochemical properties. This developed bioaugmentation/electrocoagulation process can treat wastewater with extremely high organic strength, while its approximate construction and operational costs are limited to 0.03 and 0.51 US$ m^-3, respectively. It produces a treated effluent that can be reused in irrigation of specific plants. Graphical abstract.

Microbial diversity of a Himalayan forest and characterization of rare actinomycetes for antimicrobial compounds

The slow pace of discovery of new effective drugs against multi-drug resistant pathogens and largely unsuccessful combinatorial chemistry has resulted in shifting the focus back to natural products as sources of lead molecules for antimicrobial drugs, mainly due to their structural diversity. Investigation of under-explored habitats for potentially novel microorganisms provides for wider chemodiversity. In this study, four actinomycetes, namely UK-274, UK-281, UK-282 and UK-285, which showed broad-spectrum antibacterial and antifungal activities, were isolated from Timli forest range of the biodiversity-rich Himalayan region. 16S rRNA gene sequence analysis showed that the nearest neighbours of the isolates were Actinomadura nitrigenes, Streptomyces niveiscabiei, and Kitasatospora psammotica with similarity values ranging between 97 and 98% suggesting their potential as new isolates. Further morphological and phenotypic characterization strengthened this assumption. Isolate UK-282, of the rare actinomycetes Kitasatospora group, was found to produce antimicrobial activity. Metabolite fingerprinting of ethyl acetate fraction of isolate UK-282 by GC-MS and 1H NMR analysis showed the presence of three novel compounds. The study underlines that a combination approach of bioprospecting of under-studied habitats and focus on rare actinomycetes may result in the identification of novel chemodiversity.

The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids

BACKGROUND

Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternative to antibiotic growth promoters. Altered intestinal microbiota play important roles in growth promotion, but the underlying mechanism remains unknown.

RESULTS

We generated 1.64 terabases of metagenomic data from 495 chicken intestinal digesta samples and constructed a comprehensive chicken gut microbial gene catalog (9.04 million genes), which is also the first gene catalog of an animal's gut microbiome that covers all intestinal compartments. Then, we identified the distinctive characteristics and temporal changes in the foregut and hindgut microbiota. Next, we assessed the impact of MCE on chickens and gut microbiota. Chickens fed with MCE had improved growth performance, and major microbial changes were confined to the foregut, with the predominant role of Lactobacillus being enhanced, and the amino acids, vitamins, and secondary bile acids biosynthesis pathways being upregulated, but lacked the accumulation of antibiotic-resistance genes. In comparison, treatment with chlortetracycline similarly enriched some biosynthesis pathways of nutrients in the foregut microbiota, but elicited an increase in antibiotic-producing bacteria and antibiotic-resistance genes.

CONCLUSION

The reference gene catalog of the chicken gut microbiome is an important supplement to animal gut metagenomes. Metagenomic analysis provides insights into the growth-promoting mechanism of MCE, and underscored the importance of utilizing safe and effective growth promoters.

Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 7: suitability of taxonomic units notified to EFSA until September 2017

The qualified presumption of safety (QPS) concept was developed to provide a harmonised generic pre-evaluation to support safety risk assessments of biological agents performed by EFSA's scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns identified for a taxonomic unit are, where possible and reasonable in number, considered to be 'qualifications' which should be assessed at the strain level by the EFSA's scientific Panels. No new information was found that would change the previously recommended QPS taxonomic units and their qualifications. The BIOHAZ Panel confirms that the QPS approach can be extended to a genetically modified production strain if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Between April and September 2017, the QPS notification list was updated with 46 applications for market authorisation. From these, 14 biological agents already had QPS status and 16 were not included as they are filamentous fungi or enterococci. One notification of Streptomyces K-61 (notified as former S. griseoviridis) and four of Escherichia coli were not considered for the assessment as they belong to taxonomic units that were excluded from further evaluations within the current QPS mandate. Eight notifications of Bacillus thuringiensis and one of an oomycete are pending the reception of the complete application. Two taxonomic units were evaluated: Kitasatospora paracochleata, which had not been evaluated before, and Komagataella phaffii, previously notified as Pichia pastoris included due to a change in the taxonomic identity. Kitasatospora paracochleata cannot be granted QPS status due to lack of information on its biology and to its possible production of toxic secondary metabolites. The species Komagataella phaffii can be recommended for the QPS list when used for enzyme production.