Actinobacteria in natural products research: Progress and prospects

dTSR enables efficient improvement of heterologous production of spinosad in Saccharopolyspora erythraea

Spinosad (spinosyns A and D) is a highly effective and environmentally friendly insecticide widely used for pest control. However, the difficulty of genetic manipulation in the original strain, Saccharopolyspora spinosa, has hindered improvements in fermentation yields using synthetic biology methods. Additionally, there is a lack of simple and effective methods for enhancing the production of polyketide natural products derived from slow-growing rare actinomycetes. In this study, we developed a doubly transposition and site-specific recombination (dTSR) approach to insert bacterial attachment sites (attB) and two copies of spinosad biosynthetic gene cluster (spn BGC) into various chromosomal locations of Saccharopolyspora erythraea, thereby generating heterologous production strains for screening of spinosyn producers with improved yields. Engineered strains from the first round of TSR breeding produced spinosad at levels ranging from 5.6 to 30.5 mg/L. The second round of TSR breeding produced engineered strains with increased yields, with the highest spinosad production reaching 137.1 ± 10.9 mg/L. These results indicated that (1) the dTSR approach could efficiently generate initial heterologous strains with significantly improved spinosad production, and (2) the dTSR approach enabled random integration of a second copy of spn BGC into various chromosomal locations in Sac. erythraea, thereby further increasing heterologous spinosad production to high levels. This study provides a simple, rational, and efficient approach to improve the heterologous production of polyketide natural products in rare actinomycetes.

Comparison of the start-up of rotating biofilm contactor reactor with HN-AD bacteria inoculation under high and low influent ammonia conditions

Biofilm formation is critical for the engineering application of pure biofilm RBC processes inoculated with HN-AD bacteria. This study focused on comparing the startup of pure biofilm RBC systems inoculated with HN-AD bacteria under high ammonia nitrogen (NH4+-N = 500 mg/L, H-RBC) and low ammonia nitrogen (NH4+-N = 120 mg/L, L-RBC) influent conditions. The results showed that H-RBC shortened the biofilm formation time by 6 days. Additionally, the average removal efficiencies of ammonia nitrogen and TN were 30.70 % and 38.98 % higher than those of L-RBC, respectively. High-throughput sequencing indicated that compared with L-RBC, H-RBC did not significantly change the types of HN-AD bacteria but significantly increased the abundance of the key HN-AD bacterial genera Planktosalinus and Corynebacterium. Functional gene prediction analysis showed that the abundance of key functional genes affecting the nitrogen removal process, nirS and nosZ, in H-RBC was significantly higher than in L-RBC. Phenotypic prediction analysis revealed that H-RBC could better resist changes in the external environment and had stronger nitrogen removal capacity. These findings provide a theoretical basis and effective approach for the start-up of pure biofilm RBC system.

Strategies for Actinobacteria Isolation, Cultivation, and Metabolite Production that Are Biologically Important

Novel antimicrobial agents are urgently needed to combat antimicrobial resistance from multidrug-resistant organisms. Actinobacteria are key sources of bioactive metabolites with diverse biological activities. Despite their contributions to drug discovery, the process from strain identification to drug manufacturing faces many challenges, especially the rediscovery of known compounds. Recent technological and scientific advancements have accelerated drug development. Efforts to isolate and screen rare actinobacterial species could yield novel bioactive compounds. This review summarizes techniques for selectively isolating rare actinobacteria, improving bioactive metabolite production, and discovering potential strains. Notably, new genomic strategies and new discoveries regarding spectroscopic signature-based bioactive natural products containing specific structural motifs are also discussed. Furthermore, this review updates the compounds derived from rare actinobacteria and their biological applications.

Microbial diversity and composition on the surface of Chinese alligator eggs with different phenotypes during artificial incubation

The internal and external environments affect the Chinese alligator (Alligator sinensis) eggs during the incubation period. This study aimed to explore the composition, diversity, and function of microorganisms on the surface of Chinese alligator eggs with different phenotypes during artificial incubation, providing a theoretical basis for improving the hatching success rate of Chinese alligator eggs. The development of high-throughput sequencing technology has enabled microbial DNA sequencing. In this study, the microbial community on the surface of Chinese alligator eggs (42 samples) was analyzed via 16S rRNA sequencing. The microbial profiles significantly varied among Chinese alligator eggs with a clean, shiny, crack-free surface (G group) and those with a dirty, dull, cracked surface (B group). The composition and abundance of microorganisms markedly varied between the B and G groups. The predominant bacterial taxa on the surface of Chinese alligator eggs were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidota, with Proteobacteria exhibiting the highest abundance. The abundance of Actinobacteria and Firmicutes in the G group was greater than that of the B group. Moreover, the abundance of Proteobacteria and Bacteroidota in the B group was greater than that of the G group. These findings indicate that the structure and diversity of microbial communities significantly varied on the surface of Chinese alligator eggs with different phenotypes during the incubation period and that different developmental stages of the eggs are dependent on microbes. The findings of this study provide a novel perspective on microbial dynamics during the incubation of Chinese alligator eggs and provide a scientific basis for the optimization of artificial incubation environments in the future.

Current Approaches and Implications in Discovery of Novel Bioactive Products from Microbial Sources

Bioactive Natural Products (BNPs) are in high demand due to their disease-preventive capabilities and resistance to pathogens. However, our understanding of BNP-producing microbes is limited, because many microbial populations remain uncultivated. Various approaches have been employed to explore the potential of these hidden microbes for new bioactive therapeutic compounds. Nevertheless, the possibility of discovering BNPs from microbial communities is largely cryptic due to their unculturable nature and the absence of triggers to activate the dormant Biosynthetic Gene Clusters (BGCs). Metagenome sequencing, followed by mining and characterization, is an effective approach for discovering new therapeutic BNPs. The inactive state of BGCs can be activated through the combinatorial interaction of different microbial communities within a common niche, overcoming programmable co-evolutionary stress and producing new BNPs. The present review discusses and explores the potential of hidden, uncultivated microbes for discovering novel Bioactive Natural Products (BNPs). Moreover, it provides insights into optimizing microbial production systems and fostering sustainable drug discovery and development practices by integrating multidisciplinary strategies. This review also emphasizes the critical role of microbial sources in the ongoing search for new bioactive products that can meet the demands of modern healthcare and environmental sustainability.

A Review on Rare and Symbiotic Actinobacteria: Emerging Biotechnological Tools Against Antimicrobial Resistance

Antimicrobial resistance (AMR) poses a global threat to public health, with projections estimating 10 million deaths annually by 2050 if current trends persist. Actinobacteria, renowned for their biosynthetic capacity, are a key source of bioactive compounds, producing over 75% of known antibiotics. The adaptability of these microorganisms allows them to thrive in diverse habitats, including extreme ones, through the production of secondary metabolites that are of paramount importance for industry. Furthermore, actinobacteria are capable of living in symbiosis with several organisms, producing metabolites to protect and promote the growth of the host in exchange for nutrients and shelter. Some of these metabolites, such as antibiotics, play a key role in combating host pathogens and can be biotechnologically exploited to combat human resistant pathogens. This review presents the origins of AMR, the unique biology of actinobacteria, as well as their diverse biosynthetic pathways and their role in mitigating the AMR crisis. It also highlights the need for innovative biotechnological strategies for the isolation of rare and understudied actinobacteria, as symbiotic actinobacteria, to avoid rediscovery of molecules while finding new potential natural products and scaffolds for synthetic drugs. By providing a better understanding of their ecological, genomic, and metabolic diversity, this review provides valuable insights into the exploration of rare and symbiotic actinobacteria for developing antimicrobial solutions.

Marine Natural Products in Inflammation-Related Diseases: Opportunities and Challenges

In recent decades, the potentiality of marine natural products (MNPs) in the medical field has been increasingly recognized. Natural compounds derived from marine microorganisms, algae, and invertebrates have shown significant promise for treating inflammation-related diseases. In this review, we cover the three primary sources of MNPs and their diverse and unique chemical structures and bioactivities. This review aims to summarize the progress of MNPs in combating inflammation-related diseases. Moreover, we cover the functions and mechanisms of MNPs in diseases, highlighting their functions in regulating inflammatory signaling pathways, cellular stress responses, and gut microbiota, among others. Meanwhile, we focus on key technologies and scientific methods to address the current limitations and challenges in MNPs.

MarR family regulator LcbR2 activates lincomycin biosynthesis in multiple ways

Lincomycin, produced by the actinomycete Streptomyces lincolnensis, is highly effective against Gram-positive bacteria and protozoans, making it widely used in clinical settings. This study identified LcbR2, a MarR family transcriptional regulator, as an activator of lincomycin biosynthesis. Knocking out the lcbR2 gene reduced lincomycin production by 63.0 % without affecting growth or morphology. Quantitative real-time PCR, electrophoretic mobility shift assays, and XylE reporter assays demonstrated that LcbR2 binds to a 13-bp imperfect palindromic sequence -TTGCCnnnnnCAA-, repressing the expression of lcbR2 Further analysis revealed that LcbR2 directly activates the expression of lincomycin biosynthesis genes (lmbD, lmbJ, lmbK, lmbV, and lmbW), enhancing lincomycin production. It also regulates lincomycin resistance genes (lmrA and lmrB), increasing the self-tolerance of S. lincolnensis to lincomycin. Additionally, LcbR2 modulates other regulatory genes (lmbU, adpA, aflQ1, bldD, and lcbR1), affecting lincomycin production in a cascade manner. LcbR2 also influences the expression of genes related to carbon, nitrogen, phosphorus, and sulfur metabolism, indirectly impacting lincomycin production. Moreover, the binding of LcbR2 to DNA can be attenuated by apramycin. This study thus characterized LcbR2 as a novel transcriptional regulator with a broad regulatory scope.

Seasonal dynamics and factors shaping microbiomes in freshwater finfish earthen aquaculture ponds in Bangladesh

BACKGROUND

The pondwater microbiome is believed to play a key role in fish health, including shaping mucosal surface microbiomes that help to protect against disease. How different physiochemical features relating to season, geographical locations, as well as crop species shape the pond water microbiome in the finfish aquaculture system, is not well established. Pangasius (Pangasianodon hypophthalmus) and tilapia (Oreochromis niloticus) are two of the most widely farmed fish species and disease is a major impediment to the expansion of their production. We applied 16S and 18S rRNA metabarcoding to assess how pond physicochemistry and geographical location shape water microbiomes in pangasius and tilapia aquaculture earthen ponds in Bangladesh.

RESULTS

Planctomycetota, Pseudomonadota and Actinomycetota were the dominant bacterial phyla while Stramenopiles and Alveolata were the dominant microeukaryotes (divisions) in the pangasius and tilapia ponds water. The relative abundance of Planctomycetota was higher in the pangasius ponds compared with tilapia ponds, and Actinomycetota, and Pseudomonadota were relatively higher in tilapia ponds. Tilapia pond water also exhibited a higher microbial diversity compared to that in pangasius ponds. The pondwater microbial diversity was at its lowest in winter (and/or in monsoon) and highest in the pre-monsoon period. The microbial community structures differed across the different seasons, geographical locations, culture systems, and crop species, with season and geographical locations showing the strongest effects. Of the water physicochemistry features assessed, temperature and pH were found to have a weak but significant effect on the water microbiome content for both pangasius and tilapia ponds. Pangasius and tilapia ponds shared over 46% of ASVs, and around 30% of ASVs were shared across the different study geographical locations.

CONCLUSION

Our findings demonstrate that microbial communities in pangasius and tilapia aquaculture systems in Bangladesh are shaped by season, geographical location, crop species, as well as effects from water physicochemistry. Our results provide insights into the dynamic nature and environmental influences on water microbiomes that may be applied for use in pond management for improving aquaculture productivity and enhancement of overall fish health.

Nontargeted Metabolomics of Streptomyces Sourced from Thailand Reveals the Presence of Bioactive Metabolites

Actinobacteria are widely recognized as prolific producers of bioactive metabolites with diverse biological properties, yet they remain largely unexplored. In this study, we investigated the antimicrobial potential and chemical diversity of crude extracts from actinobacterial strains isolated from mangrove sediments collected in Chonburi and Chachoengsao provinces of Thailand. Taxonomic identification confirmed that these isolates belong to the genus Streptomyces. Notably, ten isolates, identified as Streptomyces iranensis, Streptomyces yogyakartensis, Streptomyces cacaoi, Streptomyces ardesiacus, Streptomyces phaeoluteichromatogenes, and Streptomyces albiaxialis, exhibited potent inhibitory activity against chloroquine-resistant Plasmodium falciparum K1 at concentrations <10 μg/mL. Among these, only S. albiaxialis displayed anti-human immunodeficiency virus-1 viral protein R (HIV-1 Vpr) activity in HeLa cells harboring the TREx plasmid encoding full-length Vpr (TREx-HeLa-Vpr cells). MS/MS-guided molecular networking analysis highlighted the metabolic complexity of the isolates, revealing a diverse array of distinct compounds. These included chymostatin B, geldanamycin, dehydroxynocardamine, ikarugamycin epoxide, kanchanamycin C, glochidone, bisucaberin, coproporphyrin III, futalosine, and various siderophores such as ferrioxamine B, desferrioxamine D2, desferrioxamine G, desferrioxamine E, desferrioxamine, desferrioxamine H, and ferrioxamine E. Moreover, guided by the potent antimalarial activity of strain S2-SC19, the compound elaiophylin was detected, isolated, and identified using analytical techniques. Remarkably, the compound exhibited potent antimalarial activity with an IC50 value of 0.002 ± 0.002 μg/mL against P. falciparum K1. Furthermore, genomic analysis revealed that strain S2-SC19 is most closely related to Streptomyces asiaticus DSM no. 41761. This study highlights Thai mangrove soil as a valuable source of bioactive compounds, including elaiophylin, and underscores the bioactive potential and chemical diversity of mangrove ecosystems as a rich, untapped reservoir of natural products.

Subterranean marvels: microbial communities in caves and underground mines and their promise for natural product discovery

Covering: 2014 to 2024Since the dawn of human history, caves have played an intimate role in our existence. From our earliest ancestors seeking shelter from the elements to more recent generations harnessing cave substances for medicinal purposes, caves have served as essential resources and havens. The last 40 years of geomicrobiology research has replaced the outdated perception of subterranean environments as lifeless and unchanging with the realization that vibrant microbial communities have adapted to thrive in extreme conditions over millions of years. The ability of subterranean microbial communities to withstand nutrient deprivation and darkness creates a unique reservoir of untapped biosynthetic potential. These communities offer exciting prospects for medicine (e.g., antimicrobial and antitumor therapies) and biotechnology (e.g., redox chemical properties and biomineralization). This article highlights the significance of caves and mines as reservoirs of microbial diversity, the potential impact of their bioactive compounds on the fields of healthcare and biotechnology, and the significant challenges that must be overcome to access and harness the biotechnological potential of subterranean microbial communities. Additionally, it emphasizes the conservation efforts needed to protect these delicate ecosystems, ensuring the preservation of both ancient traditions and tomorrow's medicines.

Actinomycetota isolated from the sponge Hymeniacidon perlevis as a source of novel compounds with pharmacological applications: diversity, bioactivity screening, and metabolomic analysis

AIMS

To combat health conditions, such as multi-resistant bacterial infections, cancer, and metabolic diseases, new drugs need to be urgently found and, in this respect, marine Actinomycetota have a high potential to produce secondary metabolites with pharmacological importance. We aimed to study the cultivable Actinomycetota community associated with a marine sponge from the Portuguese coast, Hymeniacidon perlevis, and investigate the potential of the retrieved isolates to produce compounds with antimicrobial, anticancer and anti-obesity properties.

METHODS AND RESULTS

The analysis of the 16S rRNA gene revealed 79 Actinomycetota isolates affiliated with 12 genera-Brachybacterium, Dietzia, Glutamicibacter, Gordonia, Micrococcus, Micromonospora, Nocardia, Nocardiopsis, Paenoartrhobacter, Rhodococcus, Streptomyces, and Tsukamurella, most of which affiliated with the genus Streptomyces. The screening of antimicrobial activity revealed 13 strains, all belonging to the Streptomyces genus, capable of inhibiting the growth of Candida albicans, Bacillus subtilis, or Staphylococcus aureus. Forty-three extracts exhibited cytotoxic activity against at least one tested cell line (HepG2, HCT-116, and hCMEC-D3). Three extracts that were active against the two cancer cell lines tested, did not reduce the viability of the non-cancer endothelial cell line, hCMEC-D3. One Gordonia strain exhibited anti-obesity activity, revealed by its ability to reduce the neutral lipids in zebrafish larvae. Mass spectrometry-based dereplication analysis of active extracts identified several compounds associated with known Actinomycetota natural products. Nonetheless, five clusters contained metabolites that did not match any annotated natural products, suggesting they may represent new bioactive molecules.

CONCLUSIONS

This work contributed to increase the knowledge on the diversity and bioactive potential of Actinomycetota associated with H. perlevis.

Discovery of new aliphatic metabolites with antibacterial activities from a soil-derived Streptomyces antifungus

Fifteen new aliphatic metabolites, 2-methylpyrimidin-4(3H)-ones (1,2), 2-methoxy-2-methyl-1,2-dihydro-3H-pyrrol-3-ones (4a/4b, 5a/5b), butyrolactones (6-9), and aliphatic metabolites (16-20) as well as known pyridin-2(1H)-one (3) and butyrolactone analogues (10-15) were obtained from the fermentation broth of Streptomyces antifungus isolated from the forest soil sample collected in Tengchong, China. Pyrimidin-4(3H)-one derivatives (1, 2) with an individual 2-methylpyrimidin-4(3H)-one skeleton is a kind of rarely reported compound and were firstly obtained from natural source. The structures of the new metabolites were elucidated by comprehensive spectroscopic analysis including data from experimental and calculated ECD spectra as well as Mosher's reagent derivative method. Compounds 1, 2, 18, and 19 exhibited optimal activity against Staphylococcus aureus with MIC values ranged from 12.5 to 50 μg/mL. Further investigation revealed that 1 effectively inhibited biofilm formation and destroyed the preformed biofilm of S. aureus through oxidative damage, thereby exerting antibacterial effect.

Jejupeptins A and B: Polyketide-Cyclic Peptide Hybrids with Anti-Corticosterone Activity from Streptomyces sp. KCB15JA151

Two new polyketide-cyclic peptide hybrids jejupeptins A (1) and B (2), together with a known compound eurystatin B (3), were isolated from a culture of Streptomyces sp. KCB15JA151. The chemical structures of the compounds were elucidated using a combination of 1D and 2D NMR spectroscopy and DP4+ probability analyses. Comprehensive spectroscopic analysis revealed that 1 and 2 are the first examples of hybrid peptide-polyketides possessing an unprecedented 4-amino-3-hydroxymethyl-3-methyl-2-oxopentanoic acid moiety. A plausible biosynthetic pathway for these compounds was proposed. Biological evaluation demonstrated that compounds 1 and 2 exhibit protective effects against corticosterone-induced apoptosis and cellular oxidative stress without any associated cytotoxicity.

Rhizosphere microbiome metagenomics in PGPR-mediated alleviation of combined stress from polypropylene microplastics and Cd in hybrid Pennisetum

The simultaneous presence of microplastics (MPs) and heavy metals in soil may result in heightened toxicity, causing more significant adverse effects on plant growth. Plant growth-promoting rhizobacteria (PGPR) have demonstrated significant capacities in alleviating the toxic stress caused by the combined pollution of heavy metals and other contaminants. However, research on the impacts and processes of PGPR in alleviating stress induced by the combined pollution from MPs and heavy metals is still insufficient. This study involved a pot experiment to evaluate the ability of PGPR to mitigate stress induced by the combined pollution from polypropylene microplastic (PP MPs) particles of different sizes (6.5 μm and 830 μm) and the heavy metal cadmium (Cd) in the bioenergy plant hybrid Pennisetum. Moreover, metagenomic analysis was used to examine the effects of PGPR on the rhizospheric microbial community and function. The cocontamination of PP and Cd affected the growth of the hybrid Pennisetum differently depending on the size of the MPs particles, with the aboveground and underground lengths of the 6.5 μm PP + Cd experimental group being smaller than those of the 830 μm PP + Cd group. The PGPRs (Bacillus sp. Y-35, Bacillus sp. Y-62, Bacillus sp. Y-S, and Enterobacter sp. Y-V) successfully alleviated the stress caused by the combined pollution of PP and Cd, resulting in increases of 8.24 and 42.21% in the plant height and dry weight, respectively. The metagenomic studies indicated that the cocontamination of PP and Cd, along with PGPR inoculation, altered the composition of the rhizospheric bacterial community, leading to changes in microbial diversity indices and the composition of dominant groups such as Pseudomonadota, Actinomycetota, and Acidobacteriota. The functional analysis revealed that the main functional groups involved glucose metabolism, energy metabolism, signal transduction, and nucleotide metabolism. The MPs particle size and different PGPR significantly affected functions such as the pentose phosphate pathway, benzoate degradation, and amide biosynthesis. This study provides essential data and scientific evidence on the ecotoxicological effects of simultaneous contamination by MPs and heavy metals, as well as insights into potential bioremediation methods.

Biodegradation of oil-derived hydrocarbons by marine actinobacteria: A systematic review

The intensive use of oil and its derivatives is related to a greater frequency of accidents involving the release of pollutants that cause harmful effects on ecosystems. Actinobacteria are cosmopolitan and saprophytic microorganisms of great commercial interest, but because they are predominantly found in soil, most research into the products of this phylum's metabolism has focused on this habitat. Marine actinobacteria exhibit unique metabolic characteristics in response to extreme conditions in their habitat, which distinguishes them from terrestrial actinobacteria. This systematic review aims to describe cultivable hydrocarbonoclastic marine actinobacteria, analyze their biodegradation rates, as well as discuss their respective potential for application in bioremediation techniques and their limitations. Twenty-one actinobacteria were found to be capable of degrading one or more hydrocarbons derived from petroleum. The majority of these bacteria belonged to the genera Rhodococcus, Gordonia, Pseudonocardia, Isoptericola, Microbacterium, Citricoccus, Kocuria, Brevibacterium, and Cellulosimicrobium. The highest degradation rate was obtained by the species R. ruber, which degraded 100 % of fluorene at a concentration of 100 mg/L. On the other hand, the species Streptomyces gougerotti and Micromonospora matsumotoense were able to degrade polyethylene and use the carbon derived from it to produce polylactic acid (PLA), which represents an excellent candidate for making safely degradable bioplastics, with a view to recycling and replacing conventional petroleum-based plastics. An approach that integrates physicochemical and biological methods, and optimized growth conditions can lead to greater success in decontaminating environments. Despite the number of bacteria found in the research, this number may be significantly higher. This review provides valuable information to support further studies.

Current Approaches for Genetic Manipulation of Streptomyces spp.-Key Bacteria for Biotechnology and Environment

Organisms from the genus Streptomyces feature actinobacteria with complex developmental cycles and a great ability to produce a variety of natural products. These soil bacteria produce more than 2/3 of antibiotics used in medicine, and a large variety of bioactive compounds for industrial, medical and agricultural use. Although Streptomyces spp. have been studied for decades, the engineering of these bacteria remains challenging, and the available genetic tools are rather limited. Furthermore, most biosynthetic gene clusters in these bacteria are silent and require strategies to activate them and exploit their production potential. In order to explore, understand and manipulate the capabilities of Streptomyces spp. as a key bacterial for biotechnology, synthetic biology strategies emerged as a valuable component of Streptomyces research. Recent advancements in strategies for genetic manipulation of Streptomyces involving proposals of a large variety of synthetic components for the genetic toolbox, as well as new approaches for genome mining, assembly of genetic constructs and their delivery into the cell, allowed facilitation of the turnaround time of strain engineering and efficient production of new natural products at an industrial scale, but still have strain- and design-dependent limitations. A new perspective offered recently by technical advances in DNA sequencing, analysis and editing proposed strategies to overcome strain- and construct-specific difficulties in the engineering of Streptomyces. In this review, challenges and recent developments of approaches for Streptomyces engineering are discussed, an overview of novel synthetic biology strategies is provided and examples of successful application of new technologies in molecular genetic engineering of Streptomyces are highlighted.

Embleporicin: A Novel Class I Lanthipeptide from the Actinobacteria Embleya sp. NF3

Genome mining has emerged as a revolutionary tool for discovering new ribosomally synthesized and post-translationally modified peptides (RiPPs) in various genomes. Recently, these approaches have been used to detect and explore unique environments as sources of RiPP-producing microorganisms, particularly focusing on endophytic microorganisms found in medicinal plants. Some endophytic actinobacteria, especially strains of Streptomyces, are notable examples of peptide producers, as specific biosynthetic clusters encode them. To uncover the genetic potential of these organisms, we analyzed the genome of the endophytic actinobacterium Embleya sp. NF3 using genome mining and bioinformatics tools. Our analysis led to the identification of a putative class I lanthipeptide. We cloned the core biosynthetic genes of this putative lanthipeptide, named embleporicin, and expressed them in vitro using a cell-free protein system (CFPS). The resulting product demonstrated antimicrobial activity against Micrococcus luteus ATCC 9341. This represents the first RiPP reported in the genus Embleya and the first actinobacterial lanthipeptide produced through cell-free technology.

The complete genome sequence of Streptomyces sp. FIM 95-F1, a marine actinomycete that produces the antifungal antibiotic scopafungin

Streptomyces FIM95-F1, an actinomycete originating from mangroves of Quanzhou bay, exhibits the capability to produce the antifungal antibiotic scopafungin. Here, the complete genome of Streptomyces sp. FIM95-F1 is presented with a GC content of 71.04 %, comprising a 9,718,239-bp linear chromosome, 8236 protein-coding genes, 18 rRNA genes, 64 tRNA genes, 2 prophages, and 58 CRISPR regions. In silico analysis revealed the presence of 42 biosynthetic gene clusters (BGCs), the majority of which demonstrated similarity to both known and novel BGCs responsible for the biosynthesis of previously known and novel bioactive agents of microbial origin. A comprehensive comparison between the scopafungin BGC and niphimycin BGC has indicated a potential shared pathway for the biosynthesis of scopafungin. One of the intriguing findings of this study was the discovery of at least two novel BGCs (namely Cluster 26 and Cluster 32) present within biosynthetic gene clusters. Our findings suggest that Streptomyces sp. FIM95-F1 possesses significant potential in producing a diverse array of both known and novel bioactive compounds, which could be valuable in the field of drug discovery.

Multifunctional metabolites of Streptomyces kunmingensis BS19 from bamboo rhizosphere soil

A pigmented bioactive molecule from Streptomyces kunmingensis BS19 was isolated, characterized, and evaluated for anti-infective, antiproliferative, and wound-healing properties. The yellow-red pigment produced from the strain BS19 showed promising activity against methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium tuberculosis. Extracellular bioactive pigment from the strain BS19 was produced by agar surface fermentation and purified through bioassay guided preparative HPLC-based purification. Based on the results of UV, FT-IR, GC-MS, 1H NMR, and 13C NMR spectral analyses, the purified pigment was identified as a chromopeptide class of molecule with phenoxazinone chromophore. Its molecular weight was determined as the chemical formula C64H90N12O16 and molecular weight 1283 g/mol. It exhibited promising antimicrobial activity against Staphylococcus aureus (ATCC 1720) and antiproliferative activity against 14 types of human cancer cell lines. It showed good in vivo wound-healing activity in the rat model. The present study explored Streptomyces kunmingensis as a newly added source for the isolation of chromopeptide antibiotics for antimicrobial, wound-healing, and anticancer applications.

RS24090, a TetR family transcriptional repressor, negatively affects the rimocidin biosynthesis in Streptomyces rimosus M527

The TetR family of regulators (TFRs), commonly reported as repressors, plays a role in regulating secondary metabolite production in Streptomyces. In this study, we sought to elucidate the relationship between TFRs and rimocidin production of Streptomyces rimosus M527. Through transcriptomic analysis, we identified the protein RS24090, which exhibited significant differential expression. Phylogenetic analysis of its amino acid sequence and structural alignment predicted it to be a TetR family regulator. Thus, RS24090 was named TetR24. The role of TetR24 in biosynthesis of rimocidin was verified through gene-deletion, -complementation, and -overexpression experiments. The TetR24 gene-deletion mutant (ΔTetR24), which was generated using CRISPR/Cas9 technology, produced 38.08 % more rimocidin than the wild-type (WT) strain M527. Complementary expression of the TetR24 gene in the mutant ΔTetR24 restored rimocidin production to levels comparable to the WT strain. In contrast, the recombinant strain M527-TetR24, which harbored an overexpression of the TetR24 gene, exhibited a 40.31 % decrease in rimocidin production compared to the WT strain. A similar trend in the transcription levels of the rim genes (rimA, rimC, rimG, rimR1, and rimR2), all located in the rimocidin biosynthetic gene cluster, was revealed by quantitative RT-PCR analysis in M527-ΔTetR24, M527-ΔTetR24::TetR24, and M527-TetR24. EMSA and DNase I footprinting assays confirmed that TetR24 regulates the transcription of rim genes by binding to promoter regions of rimA and rimR2.

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

Background

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

Results

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

Conclusion

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

An Algerian Soil-Living Streptomyces alboflavus Strain as Source of Antifungal Compounds for the Management of the Pea Pathogen Fusarium oxysporum f. sp. pisi

Fusarium wilt caused by Fusarium oxysporum f. sp. pisi (Fop) poses significant threats to pea cultivation worldwide. Controlling this disease is mainly achieved through the integration of various disease management procedures, among which biological control has proven to be a safe and effective approach. This study aims to extract and identify antifungal secondary metabolites from Streptomyces alboflavus KRO3 strain and assess their effectiveness in inhibiting the in vitro growth of Fop. This bacterial strain exerts in vitro antagonistic activity against Fop, achieving highly significant inhibition over one week. The ethyl acetate extract, obtained from its ISP2 agar medium culture, also exhibited strong antifungal activity, maintaining an inhibition rate of approximately 90% at concentrations up to 250 µg/plug compared to the control. Thus, the organic extract has been fractionated using chromatographic techniques and its bioguided purification allowed us to isolate the main bioactive compound. This latter was identified as metacycloprodigiosin using nuclear magnetic resonance (NMR) spectroscopy, electrospray ionization mass spectrometry (ESI-MS), and specific optical rotation data. Metacycloprodigiosin demonstrates dose-dependent inhibitory activity against the phytopathogen with an effective concentration of 125 µg/plug. The other secondary metabolites present in the ethyl acetate extract were also identified by gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR). This study highlighted the potential of S. alboflavus KRO3 strain and its antimicrobial compounds for the management of the pea pathogen Fusarium oxysporum f. sp. pisi.

In vitro and computational investigation of antioxidant and anticancer properties of Streptomyces coeruleofuscus SCJ extract on MDA-MB-468 triple-negative breast cancer cells

This study aimed to explore the antioxidant potential of the ethyl acetate extract of Streptomyces coeruleofuscus SCJ strain, along with its inhibitory effects on the triple-negative human breast carcinoma cell line (MDA-MB-468). The ethyl acetate extract's total phenolic and flavonoid contents were quantified, and its antioxidant activity was investigated using DPPH (1,1-Diphenyl-2-picrylhydrazyl), ABTS (2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid), and FRAP (Ferric Reducing Antioxidant Power) assays. Furthermore, the cytotoxic effect of the organic extract from Streptomyces coeruleofuscus SCJ on MDA-MB-468 cancer cells was assessed via the crystal violet assay. In tandem, a thorough computational investigation was conducted to explore the pharmacokinetic properties of the identified components of the extract, utilizing the SwissADME and pKCSM web servers. Additionally, the molecular interactions between these components and Estrogen Receptor Beta, identified as a potential target, were probed through molecular docking studies. The results revealed that ethyl acetate extract of SCJ strain exhibited remarkable antioxidant activity, with 39.899 ± 1.56% and 35.798 ± 0.082% scavenging activities against DPPH and ABTS, respectively, at 1 mg/mL. The extract also displayed significant ferric reducing power, with a concentration of 1.087 ± 0.026 mg ascorbic acid equivalents per mg of dry extract. Furthermore, a strong positive correlation (p < 0.0001) between the antioxidant activity, the polyphenol and the flavonoid contents. Regarding anticancer activity, the SCJ strain extract demonstrated significant anticancer activity against TNBC MDA-MB-468 cancer cells, with an inhibition percentage of 62.76 ± 0.62%, 62.67 ± 0.93%, and 58.07 ± 4.82% at 25, 50, and 100 µg/mL of the extract, respectively. The HPLC-UV/vis analysis revealed nine phenolic compounds: gallic acid, sinapic acid, p-coumaric acid, cinnamic acid, trans-fereulic acid, syringic acid, chloroqenic acid, ellagic acid, epicatechin. Streptomyces coeruleofuscus SCJ showed promise for drug discovery, exhibiting antioxidant and anticancer effects.

Genetic Diversity and Functional Potential of Streptomyces spp. Isolated from Pachmarhi Biosphere Reserve, India

Streptomyces is a diverse genus, well known for producing a wide array of metabolites that have significant industrial utilization. The present study investigates the genetic and functional diversity of Streptomyces spp. isolated from the Pachmarhi Biosphere Reserve (PBR), India, an unexplored site. The 16S rRNA gene sequencing and analysis revealed 96 isolates belonging to 40 different species indicating a substantial phylogenetic diversity. The strains were clustered into two groups: a major cluster with 94 strains and a small cluster with two strains. BOX- PCR analyses revealed an incredible genetic diversity existing among the strains of Streptomyces spp. in PBR. The analyses revealed the intra-species diversity and inter-species closeness within the genus Streptomyces in the study area. Qualitative screening for enzyme production has shown that 53, 42, 41, 11, and 54 strains tested positive for CMCase, xylanase, amylase, pectinase, and β-glucosidase, respectively. Additionally, 54 strains tested positive for PHB production. The strains were assayed quantitatively for the production of CMCase, xylanase, amylase, and pectinase. Streptomyces sp. MP9-2, Streptomyces sp. MP10-11, Streptomyces sp. MP10-18, and Streptomyces sp. MP10-6 recorded maximum CMCase (0.604 U/mL), xylanase (0.553 U/mL), amylase (1.714 U/mL), and pectinase (13.15 U/mL) activities, respectively. Furthermore, several strains demonstrated plant growth-promoting traits, viz. zinc and phosphate solubilization and production of ammonia, HCN (hydrogen cyanide), and IAA (Indole acetic acid), and nitrogen fixation. Fifty strains showed antifungal activity against Fusarium oxysporum f. sp. lycopersici with inhibitions ranging from 7.5 to 47.5%. Current findings underscore the ecological and biotechnological significance of Streptomyces spp. in the unexplored habitat of PBR.

Biological characteristics of marine Streptomyces SK3 and optimization of cultivation conditions for production of compounds against Vibiriosis pathogen isolated from cultured white shrimp (Litopenaeus vannamei)

Antibiotic resistance in shrimp farms has emerged as an extremely serious situation worldwide. The main aim of this study was to optimize the cultural conditions for producing new antibiotic agents from marine Streptomyces species. Streptomyces SK3 was isolated from marine sediment and was identified by its 16S rDNA as well as biochemical characteristics. This microbe produced the highest concentration of bioactive secondary metabolites (BSMs) when cultured in YM medium (YM/2). It produced the maximum total protein (41.8 ± 6.36 mg/ml) during the late lag phase period. The optimum incubation temperature was recorded at 30 °C; BSMs were not produced at ≤10 °C within an incubation period of 3-4 days. The suitable agitation speed was found to be 200 rpm with pH 7.00. The proper carbon, nitrogen, and trace elements supplementation consisted of starch, malt extract, calcium carbonate (CaCO3), and magnesium sulfate (MgSO4). The ethyl acetate extract was found to act strongly against three vibriosis pathogens, Vibrio harveyi, Vibrio parahaemolyticus, and Vibrio vunificus, as indicated by the inhibition zones at 34.5, 35.4, and 34.3 mm, respectively. The extract showed the strongest anti-V. harveyi activity, as indicated by minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 0.101 ± 0.02 and 0.610 ± 0.04 mg/ml, respectively. Basic chemical investigation of the crude extract using thin layer chromatography (TLC), bioautography, liquid chromatography tandem mass spectrometry (LC‒MS/MS), Fourier transform infrared spectroscopy (FTIR), and proton nuclear magnetic resonance (1H-NMR) revealed that the active components were the terpenoid and steroid groups of compounds. They showed carboxylic acid and ester functions in their molecules.

Bioactive Insecticides from Chemometric Diverse Ant-Associated Symbionts Streptomyces novaecaesareae and Streptomyces nojiriensis against the Fall Armyworm Larvae

The Streptomyces genus has long been recognized as a prolific and valuable source of diverse secondary metabolites. These metabolites contribute significantly to the intricate chemical diversity exhibited by Streptomyces, making them an indispensable reservoir for drug discovery, agricultural applications, and industrial processes. Exploiting the potential of these natural compounds holds the promise of ushering in a new era in insect pest management, reducing reliance on synthetic chemicals and fostering ecologically sustainable solutions. This study dives into the realm of chemo diversity within isolates of Streptomyces nojiriensis and Streptomyces novaecaesareae, with a specific focus on the production of insecticidal compounds. We explored chromatographic techniques for the identification and isolation of insecticidal compounds, and two bioactive compounds were identified in extracts of S. novaecaesareae. Valinomycin was identified from hexanic extracts of strain Asp59, while naphthomycin from ethyl acetate extracts of strain Asp58. These compounds showed insecticidal activity against first instars of Spodoptera frugiperda (Asp59: LC50 = 10.82 µg/µL, LC90 = 26.25 µg/µL; Asp58: LC50 = 15.05 µg/µL, LC90 = 38.84 µg/µL). Notably, this is the first report of naphthomycin as an insecticidal compound. The present study suggests that valinomycin and naphthomycin may be a novel biological source for the control of Spodoptera frugiperda in early stages.

Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential

Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.

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

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

Drivers of the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] rhizosphere bacterial communities in Benin

Each plant species has its own rhizobacteriome, whose activities determine both soil biological quality and plant growth. Little knowledge exists of the rhizosphere bacterial communities associated with opportunity crops with high economic potential such as Synsepalum dulcificum. Native to West Africa, this shrub is famous for its red berries representing the only natural source of miraculin, a glycoprotein, with sweetening properties, but also playing a role in the treatment of cancer and diabetes. This study aimed to characterize the structure and diversity of rhizobacterial communities associated with S. dulcificum and to identify the parameters determining this diversity. An initial sampling stage allowed the collection of rhizosphere soils from 29 S. dulcificum accessions, belonging to three distinct phenotypes, from 16 municipalities of Benin, located either on farms or in home gardens. The bacterial diversity of these rhizosphere soils was assessed by Illumina sequencing of the 16S rRNA gene after DNA extraction from these soils. Furthermore, an analysis of the physicochemical properties of these soils was carried out. All accessions combined, the most represented phylum appeared to be Actinobacteriota, with an average relative abundance of 43.5 %, followed by Proteobacteria (14.8 %), Firmicutes (14.3 %) and Chloroflexi (12.2 %), yet the relative abundance of dominant phyla varied significantly among accessions (p < 0.05). Plant phenotype, habitat, climate and soil physicochemical properties affected the bacterial communities, but our study pointed out that soil physicochemical parameters were the main driver of rhizobacterial communities' structure and diversity. Among them, the assimilable phosphorus, lead, potassium, arsenic and manganese contents, texture and cation exchange capacity of rhizosphere soils were the major determinants of the composition and diversity of rhizosphere bacterial communities. These results suggested the possibility of improving the growth conditions and productivity of S. dulcificum, by harnessing its associated bacteria of interest and better managing soil physicochemical properties.

Volatile communication in Actinobacteria: a language for secondary metabolism regulation

BACKGROUND

Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group.

RESULTS

We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities.

CONCLUSIONS

This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.

A polysubstituted cyclopentane and two glycerol esters from the engineered strain Streptomyces sp. S35-LAL1

Activation of silencing gene clusters is an important way to discover structurally novel compounds. In this study, three undescribed compounds were obtained from an engineered strain of Streptomyces sp. S35-LAL1. They include a polysubstituted cyclopentane with an unprecedented 10-carbon skeleton (1) and two glycerol esters (2 and 3). The structures of compounds 1-3 were elucidated through analysis of their spectroscopic data including 1D, 2D NMR, optical rotation, and electronic circular dichroism (ECD).

Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens

The Amazon rainforest, an incredibly biodiverse ecosystem, has been increasingly vulnerable to deforestation. Despite its undeniable importance and potential, the Amazonian microbiome has historically received limited study, particularly in relation to its unique arsenal of specialized metabolites. Therefore, in this study our aim was to assess the metabolic diversity and the antifungal activity of actinobacterial strains isolated from the bulk soil of Paullinia cupana, a native crop, in the Brazilian Amazon Rainforest. Extracts from 24 strains were subjected to UPLC-MS/MS analysis using an integrative approach that relied on the Chemical Structural and Compositional Similarity (CSCS) metric, GNPS molecular networking, and in silico dereplication tools. This procedure allowed the comprehensive understanding of the chemical space encompassed by these actinobacteria, which consists of features belonging to known bioactive metabolite classes and several unannotated molecular families. Among the evaluated strains, five isolates exhibited bioactivity against a panel of soybean fungal phytopathogens (Rhizoctonia solani, Macrophomina phaseolina, and Sclerotinia sclerotiorum). A focused inspection led to the annotation of pepstatins, oligomycins, hydroxamate siderophores and dorrigocins as metabolites produced by these bioactive strains, with potentially unknown compounds also comprising their metabolomes. This study introduces a pragmatic protocol grounded in established and readily available tools for the annotation of metabolites and the prioritization of strains to optimize further isolation of specialized metabolites. Conclusively, we demonstrate the relevance of the Amazonian actinobacteria as sources for bioactive metabolites useful for agriculture. We also emphasize the importance of preserving this biome and conducting more in-depth studies on its microbiota.

Taxonomic identification and antagonistic activity of Streptomyces luomodiensis sp. nov. against phytopathogenic fungi

Banana wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is a devastating fungal disease. Biocontrol strategies hold immense potential for inhibiting the spread of Foc TR4. Here, 30 actinobacteria were isolated from soils and screened for their antagonistic activity against Foc TR4. Strain SCA4-21T was selected due to its strongest antagonistic activity against Foc TR4. Strain SCA4-21T also exhibited strong antagonistic activity against the other eight phytopathogenic fungi. The strain was identified as the genus Streptomyces according to its physiological, biochemical, and phenotypic characteristics. The phylogenetic trees of 16S rRNA sequences demonstrated that strain SCA4-21T formed a subclade with S. iranensis HM 35T and/or S. rapamycinicus NRRL B-5491T with low bootstrap values. Considering that 16S rRNAs did not provide sufficient resolution for species-level identification, the whole genome of strain SCA4-21T was sequenced. Multilocus sequence analysis (MLSA) based on five housekeeping gene alleles (atpD, gyrB, recA, rpoB, and trpB) revealed that strain SCA4-21T clustered into S. hygroscopicus subsp. hygroscopicus NBRC 13472T with 100% of bootstrap value. The analysis of the genome-based phylogeny also approved the results. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were 91.26 and 44.30%, respectively, with values below the respective species level threshold of 95 and 70%. Hence, strain SCA 4-21T represented a novel species within the genus Streptomyces, named Streptomyces luomodiensis sp. nov. The type strain is SCA4-21T (=GDMCC4.340T = JCM36555T). By the CAZymes analysis, 348 carbohydrate-active enzymes (CAZymes) were detected, including 15 chitinases and eight β-1,3-glucanases. The fermentation broth of strain SCA4-21T, exhibiting strong antagonistic activity against Foc TR4, demonstrated high activities of chitinase and β-1,3-glucanase, which might be involved in antifungal activity. Our results showed an innovative potential biocontrol agent for managing plant fungal diseases, specifically banana fusarium wilt.

Actinomycetes are a natural resource for sustainable pest control and safeguarding agriculture

Actinomycetes, a diverse group of bacteria with filamentous growth characteristics, have long captivated researchers and biochemists for their prolific production of secondary metabolites. Among the myriad roles played by actinomycete secondary metabolites, their historical significance in the field of biocontrol stands out prominently. The fascinating journey begins with the discovery of antibiotics, where renowned compounds like streptomycin, tetracycline, and erythromycin revolutionized medicine and agriculture. The history of biocontrol traces its roots back to the early twentieth century, when scientists recognized the potential of naturally occurring agents to combat pests and diseases. The emergence of synthetic pesticides in the mid-twentieth century temporarily overshadowed interest in biocontrol. However, with growing environmental concerns and the realization of the negative ecological impacts of chemical pesticides, the pendulum swung back towards exploring sustainable alternatives. Beyond their historical role as antibiotics, actinomycete-produced secondary metabolites encompass a rich repertoire with biopesticide potential. The classification of these compounds based on chemical structure and mode of action is highlighted, demonstrating their versatility against both plant pathogens and insect pests. Additionally, this review provides in-depth insights into how endophytic actinomycete strains play a pivotal role in biocontrol strategies. Case studies elucidate their effectiveness in inhibiting Spodoptera spp. and nematodes through the production of bioactive compounds. By unraveling the multifunctional roles of endophytic actinomycetes, this review contributes compelling narrative knowledge to the field of sustainable agriculture, emphasizing the potential of these microbial allies in crafting effective, environmentally friendly biocontrol strategies for combating agricultural pests.

Characterization and functional evidence for Orf2 of Streptomyces sp. 139 as a novel dipeptidase E

Aspartyl dipeptidase (dipeptidase E) can hydrolyze Asp-X dipeptides (where X is any amino acid), and the enzyme plays a key role in the degradation of peptides as nutrient sources. Dipeptidase E remains uncharacterized in Streptomyces. Orf2 from Streptomyces sp. 139 is located in the exopolysaccharide biosynthesis gene cluster, which may be a novel dipeptidase E with "S134-H170-D198" catalytic triad by sequence and structure comparison. Herein, recombinant Orf2 was expressed in E. coli and characterized dipeptidase E activity using the Asp-ρNA substrate. The optimal pH and temperature for Orf2 are 7.5 and 40 ℃; Vmax and Km of Orf2 are 0.0787 mM·min-1 and 1.709 mM, respectively. Orf2 exhibits significant degradation activities to Asp-Gly-Gly, Asp-Leu, Asp-His, and isoAsp-Leu and minimal activities to Asp-Pro and Asp-Ala. Orf2 contains a Ser-His-Asp catalytic triad characterized by point mutation. In addition, the Asp147 residue of Orf2 is also proven to be critical for the enzyme's activity through molecular docking and point mutation. Transcriptome analysis reveals the upregulation of genes associated with ribosomes, amino acid biosynthesis, and aminoacyl-tRNA biosynthesis in the orf2 mutant strain. Compared with the orf2 mutant strain and WT, the yield of crude polysaccharide does not change significantly. However, crude polysaccharides from the orf2 mutant strain exhibit a wider range of molecular weight distribution. The results indicate that the Orf2 links nutrient stress to secondary metabolism as a novel dipeptidase E. KEY POINTS: • A novel dipeptidase E with a Ser-His-Asp catalytic triad was characterized from Streptomyces sp. 139. • Orf2 was involved in peptide metabolism both in vitro and in vivo. • Orf2 linked nutrient stress to mycelia formation and secondary metabolism in Streptomyces.

Understanding and exploring the diversity of soil microorganisms in tea (Camellia sinensis) gardens: toward sustainable tea production

Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.

Streptomyces profundus sp. nov., a novel marine actinobacterium isolated from deep-sea sediment of Madeira Archipelago, Portugal

A novel strain, MA3_2.13T, was isolated from deep-sea sediment of Madeira Archipelago, Portugal, and characterized using a polyphasic approach. This strain produced dark brown soluble pigments, bronwish black substrate mycelia and an aerial mycelium with yellowish white spores, when grown on GYM 50SW agar. The main respiratory quinones were MK-10(H4), MK-10(H6) and MK-10(H8). Diphosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two glycophospholipids were identified as the main phospholipids. The major cellular fatty acids were iso-C16 : 1, iso-C16 : 0, anteiso-C17 : 1 and anteiso-C17 : 0. Phylogenetic analyses based on 16S rRNA gene showed that strain MA3_2.13T is a member of the genus Streptomyces and was most closely related to Streptomyces triticirhizae NEAU-YY642T (NR_180032.1; 16S rRNA gene similarity 97.9 %), Streptomyces sedi YIM 65188T (NR_044582.1; 16S rRNA gene similarity 97.4 %), Streptomyces mimosae 3MP-10T (NR_170412.1; 16S rRNA gene similarity 97.3 %) and Streptomyces zhaozhouensis NEAU-LZS-5T (NR_133874.1; 16S rRNA gene similarity 97.0 %). Genome pairwise comparisons with closest related type strains retrieved values below the threshold for species delineation suggesting that strain MA3_2.13T represents a new branch within the genus Streptomyces. Based on these results, strain MA3_2.13T (=DSM 115980T=LMG 33094T) is proposed as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces profundus sp. nov. is proposed.

Insights into additional lactone-based signaling circuits in Streptomyces: existence of acyl-homoserine lactones and LuxI/LuxR homologs in six Streptomyces species

Acyl-homoserine lactones (AHLs), mediating pivotal physiological activities through quorum sensing (QS), have conventionally been considered limited to Gram-negative bacteria. However, few reports on the existence of AHLs in Gram-positive bacteria have questioned this conception. Streptomyces, as Gram-positive bacteria already utilizing a lactone-based QS molecule (i.e., gamma-butyrolactones), are yet to be explored for producing AHLs, considering their metabolic capacity and physiological distinction. In this regard, our study examined the potential production of AHLs within Streptomyces by deploying HPLC-MS/MS methods, which resulted in the discovery of multiple AHL productions by S. griseus, S. lavendulae FRI-5, S. clavuligerus, S. nodosus, S. lividans, and S. coelicolor A3(2). Each of these Streptomyces species possesses a combination of AHLs of different size ranges, possibly due to their distinct properties and regulatory roles. In light of additional lactone molecules, we further confirm that AHL- and GBL-synthases (i.e., LuxI and AfsA enzyme families, respectively) and their receptors (i.e., LuxR and ArpA) are evolutionarily distinct. To this end, we searched for the components of the AHL signaling circuit, i.e., AHL synthases and receptors, in the Streptomyces genus, and we have identified multiple potential LuxI and LuxR homologs in all 2,336 Streptomyces species included in this study. The 6 Streptomyces of interest in this study also had at least 4 LuxI homologs and 97 LuxR homologs. In conclusion, AHLs and associated gene regulatory systems could be more widespread within the prokaryotic realm than previously believed, potentially contributing to the control of secondary metabolites (e.g., antibiotics) and their complex life cycle, which leads to substantial industrial and clinical applications.

Metabolic perturbation of Streptomyces albulus by introducing NADP-dependent glyceraldehyde 3-phosphate dehydrogenase

The available resources of Streptomyces represent a valuable repository of bioactive natural products that warrant exploration. Streptomyces albulus is primarily utilized in the industrial synthesis of ε-poly-L-lysine (ε-PL). In this study, the NADP-dependent glyceraldehyde 3-phosphate dehydrogenase (GapN) from Streptococcus mutans was heterologously expressed in S. albulus CICC11022, leading to elevated intracellular NADPH levels and reduced NADH and ATP concentrations. The resulting perturbation of S. albulus metabolism was comprehensively analyzed using transcriptomic and metabolomic methodologies. A decrease in production of ε-PL was observed. The expression of gapN significantly impacted on 23 gene clusters responsible for the biosynthesis of secondary metabolites. A comprehensive analysis revealed a total of 21 metabolites exhibiting elevated levels both intracellularly and extracellularly in the gapN expressing strain compared to those in the control strain. These findings underscore the potential of S. albulus to generate diverse bioactive natural products, thus offering valuable insights for the utilization of known Streptomyces resources through genetic manipulation.

Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria

Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.

Animal Microbiomes as a Source of Novel Antibiotic-Producing Strains

Natural compounds continue to serve as the most fruitful source of new antimicrobials. Analysis of bacterial genomes have revealed that the biosynthetic potential of antibiotic producers by far exceeds the number of already discovered structures. However, due to the repeated discovery of known substances, it has become necessary to change both approaches to the search for antibiotics and the sources of producer strains. The pressure of natural selection and the diversity of interactions in symbiotic communities make animal microbiomes promising sources of novel substances. Here, microorganisms associated with various animals were examined in terms of their antimicrobial agents. The application of alternative cultivation techniques, ultrahigh-throughput screening, and genomic analysis facilitated the investigation of compounds produced by unique representatives of the animal microbiota. We believe that new strategies of antipathogen defense will be discovered by precisely studying cell-cell and host-microbe interactions in microbiomes in the wild.

OSMAC Method to Assess Impact of Culture Parameters on Metabolomic Diversity and Biological Activity of Marine-Derived Actinobacteria

Actinobacteria are known for their production of bioactive specialized metabolites, but they are still under-exploited. This study uses the "One Strain Many Compounds" (OSMAC) method to explore the potential of three preselected marine-derived actinobacteria: Salinispora arenicola (SH-78) and two Micromonospora sp. strains (SH-82 and SH-57). Various parameters, including the duration of the culture and the nature of the growth medium, were modified to assess their impact on the production of specialized metabolites. This approach involved a characterization based on chemical analysis completed with the construction of molecular networks and biological testing to evaluate cytotoxic and antiplasmodial activities. The results indicated that the influence of culture parameters depended on the studied species and also varied in relation with the microbial metabolites targeted. However, common favorable parameters could be observed for all strains such as an increase in the duration of the culture or the use of the A1 medium. For Micromonospora sp. SH-82, the solid A1 medium culture over 21 days favored a greater chemical diversity. A rise in the antiplasmodial activity was observed with this culture duration, with a IC50 twice as low as for the 14-day culture. Micromonospora sp. SH-57 produced more diverse natural products in liquid culture, with approximately 54% of nodes from the molecular network specifically linked to the type of culture support. Enhanced biological activities were also observed with specific sets of parameters. Finally, for Salinispora arenicola SH-78, liquid culture allowed a greater diversity of metabolites, but intensity variations were specifically observed for some metabolites under other conditions. Notably, compounds related to staurosporine were more abundant in solid culture. Consequently, in the range of the chosen parameters, optimal conditions to enhance metabolic diversity and biological activities in these three marine-derived actinobacteria were identified, paving the way for future isolation works.

The assembly of gut microbiota implicates shrimp acute hepatopancreas necrosis disease progression

Ample evidence shows dysbiosis in the gut microbiota when comparing healthy shrimp with those affected by severe acute hepatopancreatic necrosis disease (AHPND). However, the static comparison used in available studies leads to the uncertainties regarding how and to what extent the gut microbiota responds to the progressive severity of AHPND. In addition, shrimp AHPND is featured by rapid and massive mortality, thus the initiation of AHPND must be diagnosed for preemptive therapy. For these reasons, we explored the ecological assembly of gut microbiota over shrimp AHPND progression. Increasing AHPND severity was associated with linear increase in the copies of pirAB genes, relative abundance of gut Vibrio and potentially pathogenic, and reduction in the gut bacterial diversity, stability, and relative abundance of Bdellovibrio. Negative and significant association between gut Vibrio and Bdellovibrio were noted, indicating that compromised predation exerts a role in AHPND progression. Notably, the extents of departure to the healthy shrimp gut microbiota were positively coupled with the increasing severity of AHPND. After controlling the temporal variation in the gut microbiota as healthy shrimp age, we constructed a diagnosis model that accurately diagnosed the initial, progressed or moribund stages of AHPND, with an overall accuracy of 86.5%. Shrimp AHPND induced more stochastic gut microbiotas as a consequence of the attenuated ability of diseased shrimp to select their commensals, resulting in convergent bacterial communities between gut and rearing water over AHPND progression. Collectively, our findings provide important step toward the ecological assembly of gut microbiota implicating in AHPND etiology and in diagnosing AHPND stages. KEY POINTS: • The departure of shrimp gut microbiota positively linked with AHPND severity. • The diagnosis model accurately diagnosed the stages of AHPND. • Shrimp AHPND induced more stochastic gut microbiota.

Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens

Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.

LcbR1, a newly identified GntR family regulator, represses lincomycin biosynthesis in Streptomyces lincolnensis

The Actinomycetes Streptomyces lincolnensis is the producer of lincosamide-type antibiotic lincomycin, a widely utilized drug against Gram-positive bacteria and protozoans. In this work, through gene knockout, complementation, and overexpression experiments, we identified LcbR1 (SLINC_1595), a GntR family transcriptional regulator, as a repressor for lincomycin biosynthesis. Deletion of lcbR1 boosted lincomycin production by 3.8-fold, without obvious change in morphological development or cellular growth. The homologues of LcbR1 are widely distributed in Streptomyces. Heterologous expression of SCO1410 from Streptomyces coelicolor resulted in the reduction of lincomycin yield, implying that the function of LcbR1 is conserved across different species. Alignment among sequences upstream of lcbR1 and their homologues revealed a conserved 16-bp palindrome (-TTGAACGATCCTTCAA-), which was further proven to be the recognition motif of LcbR1 by electrophoretic mobility shift assays (EMSAs). Via this motif, LcbR1 suppressed the transcription of lcbR1 and SLINC_1596 sharing the same bi-directional promoter. SLINC_1596, one important target of LcbR1, exerted a positive effect on lincomycin production. As detected by quantitative real-time PCR (qRT-PCR) analyses, the expressions of all selected structural (lmbA, lmbC, lmbJ, lmbV, and lmbW), resistance (lmrA and lmrB) and regulatory genes (lmrC and lmbU) from lincomycin biosynthesis cluster were upregulated in deletion strain ΔlcbR1 at 48 h of fermentation, while the mRNA amounts of bldD, glnR, ramR, SLCG_Lrp, and SLCG_2919, previously characterized as the regulators on lincomycin production, were decreased in strain ΔlcbR1, although the regulatory effects of LcbR1 on the above differential expression genes seemed to be indirect. Besides, indicated by EMSAs, the expression of lcbR1 might be regulated by GlnR, SLCG_Lrp, and SLCG_2919, which shows the complexity of the regulatory network on lincomycin biosynthesis. KEY POINTS: • LcbR1 is a novel and conservative GntR family regulator regulating lincomycin production. • LcbR1 modulates the expressions of lcbR1 and SLINC_1596 through a palindromic motif. • GlnR, SLCG_Lrp, and SLCG_2919 can control the expression of lcbR1.

Characterization and biocontrol mechanism of Streptomyces olivoreticuli as a potential biocontrol agent against Rhizoctonia solani

Rhizoctonia solani is a widespread and devastating plant pathogenic fungus that infects many important crops. This pathogen causes tobacco target spot, a disease that is widespread in many tobacco-growing countries and is destructive to tobacco. To identify antagonistic microorganisms with biocontrol potential against this disease, we isolated Streptomyces strains from forest inter-root soil and screened a promising biocontrol strain, ZZ-21. Based on in vitro antagonism assays, ZZ-21 showed a significant inhibitory effect on R. solani and various other phytopathogens. ZZ-21 was identified as Streptomyces olivoreticuli by its phenotypic, genetic, physiological and biochemical properties. Complete genome sequencing revealed that ZZ-21 harbored numerous antimicrobial biosynthesis gene clusters. ZZ-21 significantly reduced the lesion length in detached inoculated leaf assays and reduced the disease index under greenhouse and field conditions. Based on an in vitro antagonistic assay of ZZ-21 culture, the strain exhibited an antifungal activity against R. solani in a dose-dependent manner. The culture filtrate could impair membrane integrity, possibly through membrane lipid peroxidation. ZZ-21 could secrete multiple extracellular enzymes and siderophores. According to a series of antifungal assays, the extracellular metabolites of ZZ-21 contained antimicrobial bioactive compounds composed of proteins/peptides extracted using ammonium sulfate precipitation, which were stable under stress caused by high temperature and protease K. The EC50 value for ammonium sulfate precipitation was determined to be 21.11 μg/mL in this study. Moreover, the proteins/peptides also exhibited biocontrol ability and were observed to alter the plasma membrane integrity of R. solani which were evaluated by biocontrol efficacy assays on detached tobacco leaves and PI staining. Overall, strain ZZ-21 shows the potential to be developed into a biopesticide against tobacco target spot disease.

Antibacterial and Anti-HIV Metabolites from Marine Streptomyces albus MAB56 Isolated from Andaman and Nicobar Islands, India

Marine-derived actinobacteria have tremendous potential to produce novel metabolites with diverse biological activities. The Andaman coast of India has a lot of microbial diversity, but it is still a relatively unknown ecology for isolating novel actinobacteria with beneficial bioactive compounds. We have isolated 568 actinobacterial strains from mangrove rhizosphere sediments and sponge samples. Crude extracts from 75 distinct strains were produced by agar surface fermentation and extracted using ethyl acetate. In the disc diffusion method, 25 actinobacterial strains showed antimicrobial activity; notably, the strain MAB56 demonstrated promising broad-spectrum activity. Strain MAB56 was identified as Streptomyces albus by cultural, microscopic, and molecular methods. Conditions for bioactive metabolites from MAB56 were optimized and produced in a lab-scale fermenter. Three active metabolites (C1, C2, and C3) that showed promising broad-spectrum antimicrobial activity were isolated through HPLC-based purification. Based on the UV, FT-IR, NMR, and LC-MS analysis, the chemical nature of the active compounds was confirmed as 12-methyltetradecanoic acid (C1), palmitic acid (C2), and tridecanoic acid (C3) with molecular formulae C14H28O2, C16H32O2, and C13H26O2, respectively. Interestingly, palmitic acid (C2) also exhibited anti-HIV activity with an IC50 value of < 1 µg/ml. Our findings reveal that the actinobacteria from the Andaman marine ecosystems are promising for isolating anti-infective metabolites.

Effects of feed additives on rumen function and bacterial and archaeal communities during a starch and fructose challenge

The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 1012 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.