Authors: Soumia Ait Assou (Department of Biology, Biotechnology, Environment, Agri-Food and Health Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco), Mohammed El Hassouni (Department of Biology, Biotechnology, Environment, Agri-Food and Health Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco)
Categories: Review Article, antibacterial activity, Gram-positive bacteria, natural products, Streptomyces
Source: The Scientific World Journal
Doi: 10.1155/tswj/6659874
Authors: Soumia Ait Assou, Mohammed El Hassouni
Bacterial infections, particularly those caused by Gram-positive bacteria like vancomycin-resistant enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA), are a growing concern. This review highlights the potential of the Streptomyces genus in producing novel antibacterial compounds against Gram-positive bacteria. The study was carried out following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). To gather relevant literature on novel anti-Gram-positive bacteria compounds produced by Streptomyces, a web search was conducted using several databases, including Scopus, PubMed, ScienceDirect, and Google Scholar, covering the period from January 2013 to mid-2024. The search terms employed in this study included “Streptomyces,” “antimicrobial/antibacterial activity,” “compounds,” and “Gram-positive bacteria.” Consequently, a total of 248 Streptomyces-derived compounds were featured across the 96 eligible studies. These compounds include 100 polyketides (58 aromatic polyketides, 30 macrolides, and 12 other polyketides), 72 peptides (67 nonribosomal peptides [52 typical cyclic peptides and 15 lipopeptides] and 5 ribosomal peptides), 23 terpenoids, five polyketides–terpenoids, six alkaloids, 12 phenazines, 11 nucleoside antibiotics, and 19 other compounds belonging to distinct chemical classes. The results emphasize that Streptomyces is an unlimited source of naturally occurring compounds with various structural variations that can occasionally have targeted action against a range of pathogenic Gram-positive bacteria.
One of the most significant public health issues that has to be addressed globally is antimicrobial resistance (AMR) [1, 2]. According to a 2016 UK government report, AMR may kill 10 million people annually by 2050 [3]. Multidrug-resistant microbial strains, some resistant to first-line antibiotics, are becoming more prevalent as antibiotic efficacy continues to decline [4].
Multidrug resistance in Gram-negative bacteria has received a lot of attention worldwide, but Gram-positive bacteria are also a major concern [5]. The World Health Organization (WHO) recently published a global priority pathogen list and categorized them as critical, high, and medium antibiotic-resistant bacteria based on the urgent need for new antibiotics [6]. Multidrug-resistant bacteria like vancomycin-resistant Enterococcus faecium (VREfm) and MRSA stand out among the most common Gram-positive bacteria that can cause serious infections and are regarded as a major problem and health hazard [6]. Because of the emergence of these multidrug-resistant bacteria, it is crucial to increase research and development efforts to discover and develop new antibiotics as well as look into alternative treatment options [7].
Since Fleming's unintentional discovery of penicillin in 1928, microorganisms have provided a never-ending source of bioactive compounds with a wide range of biological functions, most notably antimicrobial activity. In fact, bacteria are the primary source of the majority of antibiotics available on the market. With around 12,000 known bioactive metabolites, actinomycetes are among the most abundant bacteria for producing bioactive compounds, including antibiotics. Approximately 80% of these metabolites are produced by the Streptomyces genus, making it the greatest producer [8].
Numerous biosynthetic gene clusters (BGCs) are closely linked to the production of secondary metabolites by actinomycetes, especially Streptomyces, according to genomic investigations of these bacteria. According to Nett et al. [9], between half and three-quarters of these BGCs encode enzyme complexes, such as nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), and their hybrid compounds. It is interesting to note that despite having a similar biosynthesis process, polyketides generated by various actinomycete strains exhibit notable chemodiversity [10]. Numerous biological actions exhibited by these metabolites have been established for the synthesis of various medications, primarily antibiotics [11].
This review aims to identify antibacterial compounds active specifically against Gram-positive bacteria, derived from the Streptomyces genus, discovered between 2013 and mid-2024. It emphasizes the isolation source of the Streptomyces species/strains, the chemical classes of bioactive compounds, and their antibacterial activity, as well as the most potent compounds and their chemical structures.
Some studies have specifically reviewed Gram-positive bacteria inhibited by compounds derived from marine Actinobacteria, such as anti-Listeria compounds [12] or the work of Kemung et al. [13] on potential drug candidates against MRSA derived from the Streptomyces strains with a focus on those from only underexplored biotopes. Additionally, several studies have focused on specific classes of novel compounds from marine actinomycetes or the Streptomyces genus [14, 15]. Some studies focused on compounds from Streptomyces with various biological activities, specifically over the course of 1 year. For example, Lacey and Rutledge [16] conducted a review on new Streptomyces compounds, reviewing studies published in 2020 that investigated a range of biological activities.
Our study stands out with a distinctive approach. It consolidates information exclusively on new anti-Gram-positive bacteria compounds derived from Streptomyces species or strains isolated from diverse environments and biotopes. By focusing on compounds identified between January 2013 and mid-2024, this review offers a clear classification of these compounds. Our aim is to provide the scientific community with a solid knowledge base, facilitating future research efforts and enabling the identification of promising compounds with significant therapeutic potential.
This review was performed according to the PRISMA checklist. We carried out a thorough and systematic search across multiple databases to identify all relevant studies on novel antibacterial compounds against Gram-positive bacteria, produced by the Streptomyces genus, over the past decade (from January 2013 to June 2024). A deep search was conducted via the databases PubMed (http://www.ncbi.nlm.nih.gov/pubmed), Google Scholar (http://scholar.google.com), Scopus (http://www.scopus.com), and online collection ScienceDirect (http://www.sciencedirect.com). Articles in the English language were searched using different phrases in combination using Boolean operators (“OR”/“AND”) such as “Streptomyces,” “antimicrobial/antibacterial activity,” “compounds,” and “Gram-positive bacteria.” The search methodology was illustrated following PRISMA 2020 method guidelines along with the studies included or excluded, explaining the reasons for exclusion.
To obtain representative information, inclusion and exclusion criteria were applied when searching for scientific articles. ➢Inclusion criteria
i. Compounds from Streptomyces spp. that were tested for antibacterial activity.ii. Anti-Gram-positive bacteria activity was from Streptomyces spp. compounds.iii. Antibacterial activity reported in MIC value.➢Exclusion criteria
i. Not a compound produced by Streptomyces sp.ii. Using different techniques apart from the minimum inhibitory concentration (MIC) 50% inhibitory concentration (IC50), 50% minimum inhibitory concentration (MIC50), 90% minimum inhibitory concentration (MIC90), and the diameter of inhibition zone (DIZ).iii. Broad spectrum of activity (anti-Gram-negative bacteria and or anti-fungi).
The authors conducted an independent review of titles and abstracts to evaluate their relevance based on defined inclusion criteria. Full texts of studies that satisfied these criteria were then obtained for a more thorough assessment. Both authors engaged in this full-text screening, collaboratively resolving any disagreements through discussion and consensus. Following this screening, a final selection of studies was chosen for inclusion in the review, ensuring that all met the eligibility criteria and aligned with the review's objectives. The initial screening and data extraction were led by the first author, S.A.A., while the second author, M.E.H., provided guidance and oversight throughout the process. Ultimately, both authors participated in the final decision-making to address any discrepancies in the study selection.
The data was collected by the first author (S.A.A.). To ensure accuracy and consistency, all extracted data underwent a thorough double-checking. Any discrepancies were addressed through discussions between the two authors. The variables extracted included the publication year, Streptomyces species or strain, isolation source (such as marine sediment, soil, and endophyte), the Gram-positive bacteria tested, the chemical class of each bioactive compound and its MIC value, and the structures of the most potent compounds. When MIC values were reported in molar units, they were converted to microgram per milliliter using the molecular weight of each compound to ensure consistency across the studies.
This review focuses on the antibacterial activity of natural products from Streptomyces species or strains. Consequently, the majority of the studies included are experimental laboratory studies rather than clinical trials or observational studies. As a result, conventional tools for assessing methodological bias are not applicable.
The extracted data were synthesized qualitatively due to the heterogeneity of study designs, compound classes, and target bacterial strains involved. Antibacterial activity was grouped and summarized according to the chemical class of the compounds. To provide a clear overview, for each chemical class, a summary table was constructed to present MIC values alongside the corresponding Streptomyces strains or species, their isolation sources, and the targeted Gram-positive bacteria. Compounds with particularly low MIC values were highlighted, and their chemical structures were included. No statistical meta-analysis was carried out.
Figure 1 demonstrates the article selection method, PRISMA 2020 [17]. The literature search identified 242 scientific articles. A screening process was then conducted to select only those relevant to the study. In the initial screening, 107 articles were excluded because the reported compounds exhibited a broad spectrum of activity, inhibiting both Gram-negative bacteria and fungal strains, or exhibiting no activity. This step resulted in 115 articles being retained for further evaluation. During the second screening phase, only articles reporting antibacterial activity against Gram-positive bacteria with clearly defined MIC values were retained. A further 19 articles were excluded, due to inconsistent reporting formats such as IC50, MIC50, MIC99, or percentage-based values. Therefore, only 96 of the studies met the eligibility criteria and were considered in the final systematic review (Figure 1).
The included articles in this study focused on the isolation of one or more compounds derived from a single strain or species of Streptomyces. To assess antibacterial activity, all studies employed in vitro laboratory methods, particularly the broth microdilution method, and reported MIC values in microgram per milliliter. The Gram-positive bacterial strains examined across all the articles include, in particular, strains of Staphylococcus (aureus, saprophyticus, epidermidis, haemolyticus, warneri, and simulans), Bacillus (subtilis, cereus, anthracis, thuringiensis, and megaterium), Enterococcus (faecalis, faecium, hirae, and gallinarum), Micrococcus luteus, Listeria (monocytogenes and ivanovii subsp. ivanovii), Mycobacterium (tuberculosis, smegmatis, intracellulare, bovis, avium, abscessus, and aurum), Streptococcus (agalactiae, pneumoniae, pyogenes, and anginosus), Lactobacillus (brevis, bulgaricus, and sakei subsp. sakei), Clostridium (difficile, bifermentans, butyricum, indolis, innocuum, limosum, perfringens, and ramosum), and Kocuria rhizophila.
In reviewing the 96 publications, it was found that 93 studies reported on a distinctive species or strain, while the remaining three studies focused, each one, on a single strain that was also among the 93 distinctive strains. As a result, 93 strains were documented, originating from different environmental sources. Figure 2 illustrates this diversity, showing that the isolation sources range from terrestrial environments (soil, acidic mine drainage, plants, insects, and animals) to marine environments (marine sediments, sponges, and corals). Marine sediments alone account for 33.33% (n = 31) of the described Streptomyces strains, followed by terrestrial soil with 21.50% (n = 20). Notably, a significant proportion of the publications (18.27%, n = 17) did not specify the environmental source of the Streptomyces strain (Figure 2).
The 96 articles included in the present review were further analyzed, leading to the identification of 248 compounds classified into several classes.
Polyketides constitute a diverse class of natural metabolites characterized by multiple β-hydroxyketone or β-hydroxyaldehyde groups. These compounds are synthesized by enzymatic complexes known as PKSs.
In Streptomyces, three main types of PKSs (Type I, Type II, and Type III) are responsible for polyketide biosynthesis. Type I PKSs specifically produce macrolides, while Type II PKSs are involved in the synthesis of aromatic polyketides. Based on their polyphenolic cyclic systems and biosynthetic pathways, aromatic polyketides are further classified into three major anthracyclines, angucyclines, and tetracyclines, alongside several other diverse subclasses [18, 19].
As illustrated in Figure 3, polyketides represent the most isolated class of anti-Gram-positive bacterial compounds from the Streptomyces genus since 2013, with 100 compounds identified, accounting for 40.32% of the total compounds (Figure 3a). These polyketides are subdivided • Aromatic representing the largest subclass, with 58 compounds (58%), primarily including angucyclines, anthracyclines, and xanthones.• Macrolides: the second-largest subclass, comprising 30 molecules (30%).• Other a diverse group of 12 compounds (12%) belonging to various other polyketide families (Figure 3b).
Microbial peptides with antimicrobial activity are categorized into two main nonribosomal peptides (NRPs) and ribosomal peptides. • NRPs: These are structurally diverse secondary metabolites produced by fungi and bacteria through multimodular enzymes called NRPSs, independently of ribosomes [20]. NRPs principally include cyclic peptides (typically composed of two to eight amino acids) and lipopeptides. These peptides have either linear or cyclic structures, characterized by an N-terminus hydrophobic fatty acid tail [21].• Ribosomal These peptides are ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs). They mainly include lassopeptides, thiopeptides, and lanthipeptides. Lassopeptides have a macrocyclic ring formed by seven to nine N-terminal amino acid residues that trap the C-terminus [22]. Thiopeptides (or thiazolyl peptides) are sulfur-rich peptides [23]. Lanthipeptides are distinguished by thioether-bridged amino acids, such as lanthionine (Lan) and methyllanthionine (MeLan) [24].
Since 2013, 72 peptide compounds (29.03%) derived from Streptomyces with specific activity against Gram-positive bacteria have been identified (Figure 3): • NRPs: with 67 (52 cyclic peptides [72.22%] and 15 lipopeptides [20.83%]).• RiPPs: with five (6.94%), represented by lassopeptides, thiopeptides, and lanthipeptides (Figure 3c).
Terpenoids are natural chemical compounds synthesized through the condensation of isopentenyl diphosphate (IPP) and its isomer, dimethylallyl diphosphate (DMAPP). Meroterpenoids and diterpenoids mainly represent them. Among the meroterpenoids, napyradiomycins form a prominent subclass. While numerous terpenoid metabolites have been isolated from plants and fungi, bacterial terpenoids remain relatively rare [25]. Except for geosmin, a terpene responsible for the characteristic earthy odor of Streptomyces, these bacteria are considered a limited source of terpenes [26]. As shown in Figure 3a, terpenoids represent the third-largest class (23 compounds [9.27%]) of compounds exhibiting specific activity against Gram-positive bacteria, isolated from the Streptomyces genus since 2013.
Polyketides–terpenoids are hybrid natural products derived from both polyketide and terpenoid biosynthetic pathways. Over the past decade, five (2.01%) polyketides–terpenoids with antibacterial activity against Gram-positive bacteria have been identified (Figure 3a).
Alkaloids are the main secondary metabolites of actinomycetes and one of the most medicinal types of compounds. Most of these nitrogen-containing molecules possess complex ring structures with important pharmacological activity [27]. In this review, six alkaloids (2.41%), targeting Gram-positive bacteria, were isolated from the Streptomyces genus over the past decade (Figure 3a).
Phenazines are a large family of nitrogen-containing natural compounds characterized by two benzene rings linked via two nitrogen atoms. They exhibit a wide range of biological activities, including antibacterial, antitumor, and antiparasitic properties [28]. In this review, we report the identification of 12 new phenazines (4.83%) specifically inhibiting Gram-positive bacteria, isolated from the Streptomyces genus over the past decade, from 2013 to mid-2024 (Figure 3a).
Nucleoside antibiotics are an important family of microbial natural products derived from nucleosides and nucleotides. They exhibit various biological activities, such as antibacterial, antifungal, antiviral, insecticidal, immunostimulative, and antitumor activities. Nucleoside antibiotics can be grouped into two classes, C-nucleosides and N-nucleosides, in which a sugar and a nucleobase are linked via a C–C bond or a C–N bond, respectively [29]. Over the past decade, 11 (4.43%) nucleoside antibiotics with antibacterial activity against Gram-positive bacteria have been identified (Figure 3a).
In addition to the aforementioned classes, 19 other compounds (7.66%) with activity against Gram-positive bacteria have been isolated over the past decade (Figure 3a). These compounds belong to distinct chemical classes, including dimeric cinnamoyl lipids, liposidomycin congeners, siderophores, gilvocarcin-type aryl-C-glycosides, and tetracene derivatives.
The antibacterial activity of the 248 novel compounds was analyzed according to their chemical classification. It is important to note that some compounds exhibited additional biological activities, including cytotoxic activity against tumor cells (22.98%, n = 57), antiviral activity (1.61%, n = 4), and acetylcholinesterase inhibitory activity (1.61%, n = 4) in addition to their antibacterial effect against Gram-positive bacteria (Figure 4).
In the following section, the previously unidentified compounds with exclusive activity against Gram-positive bacteria that were first isolated from the Streptomyces genus, since 2013 to mid-2024, are listed according to their chemical classification, along with the description of the potent ones, their chemical structures, and their structure–activity relationships (SARs), if available.
As shown in Table 1, there have been numerous reports of aromatic polyketides produced by the Streptomyces genus during the last decade, with a total of 58 compounds. These polyketides belong to different families (angucyclines, anthracyclines, xanthones, etc.) and show antibacterial activity against Gram-positive bacteria, including MRSA and VRE.
Aromatic polyketide compounds with the lowest MIC values and therefore effective concentrations were derived from the terrestrial Streptomyces CPCC 204980. This species produced four notable polycyclic xanthones, namely, cervinomycins B1−4, which showed very good anti-Gram-positive bacteria activity, with MICs ranging from 0.008 to 0.5 μg/mL against S. aureus ATCC 33591, S. aureus 16-30, Enterococcus faecalis ATCC 51299, and E. faecium ATCC 700221 (Table 1 and Figure 5) [30].
Another group of highly polycyclic xanthones, known as kebanmycins A–C, was isolated from a mangrove-derived actinomycete, Streptomyces sp. SCSIO 40068 (Figure 5). These compounds exhibited significant antibacterial activity against several strains of S. aureus (ATCC 29213, MRSA shhs-A1, MRSA 1862, MRSA 669, and MRSA 991) with MICs of 0.125–0.5 μg/mL for kebanmycin A, 1–2 μg/mL for kebanmycin B, and 0.5–4 μg/mL for kebanmycin C. Notably, kebanmycin B displayed the strongest activity against Bacillus subtilis 1064, with an MIC of 1 μg/mL, while kebanmycin A and kebanmycin C showed MICs of > 64 and 4 μg/mL, respectively (Table 1) [31].
From a new Streptomyces species, named S. formicae, isolated from the African fungus-growing plant-ant Tetraponera penzigi, 15 novel pentacyclic polyketides were purified. Among them, formicamycins I, K, and L stand out as the most potent, displaying antibacterial activity against B. subtilis, MRSA, and VREfm with MIC values ranging from 0.80 to 3.26 μg/mL (1.25–5 μM) (Table 1 and Figure 5) [32]. To examine their SAR, the growth of B. subtilis was examined in liquid media supplemented with 0.01–100 μM of isolated formicamycins. Dose–response analyses showed that all compounds effectively inhibit the growth of B. subtilis, with enhanced effectiveness noted for compounds containing an increasing number of chlorine atoms (formicamycins D–L). Notably, the brominated compounds (formicamycins K and L) appear to exhibit a slightly greater potency compared to their chlorinated counterparts [32].
Additional strongly aromatic polyketide compounds were fasamycins isolated from S. morookaense. This strain produced eight fasamycins compounds designated streptovertimycins A–H (Figure 5). These compounds show strong inhibitory potential at low concentrations, such as streptovertimycin G at 0.63 and 1.25 μg/mL against MRSA and VREfm, respectively (Table 1) [33]. Comparative SAR analysis suggests that a free hydroxyl group at C-3 is beneficial for the activity. Furthermore, the 5-O-methyl bearing streptovertimycin G increases potency two- to four-fold compared to its 5-OH variant (streptovertimycin F) [33].
Macrolides are a large family of natural products with various biological activities that have attracted interest from the pharmaceutical community [50]. Most macrolide antibiotics are typically characterized by a lactone ring and one or more sugar moieties. Over the past decade, 30 novel macrolides with antibacterial activity against Gram-positive bacteria have been identified from the Streptomyces genus (Table 2).
One remarkable discovery is anthracimycin (Figure 6), a macrolide isolated from Streptomyces sp. CNH365, derived from marine sediments of the coast of Santa Barbara in the Pacific Ocean. Anthracimycin demonstrates potent inhibitory activity against Gram-positive bacteria, particularly Bacillus anthracis (strain UM23C1-1), with an exceptionally low minimum MIC value of 0.031 μg/mL, and 0.0625 and 0.125 μg/mL against S. aureus ATCC 13709 and E. faecalis ATCC 29212, respectively (Table 2) [51].
Five years later, a structurally related compound, anthracimycin B (Figure 6), was isolated from the deep-sea S. cyaneofuscatus M-169 through bioassay-guided fractionation. Although less potent than anthracimycin, anthracimycin B still exhibited significant antibacterial activity against tested pathogens (S. aureus MB5393 [MRSA] and ATCC 29213 [MSSA]), vancomycin-sensitive E. faecium CL144754 (VSE), and E. faecalis CL144492 (VSE) with MIC values ranging from 0.125 to 8 μg/mL (Table 2) [52]. A preliminary SAR hypothesis suggests that the methyl group at C-2 present in anthracimycin plays an important role in its strong antibacterial activity in comparison with anthracimycin B [52].
Another noteworthy group is the spirotetronate macrolides, recognized for their complex chemical structures, diverse biological activities, and promising pharmacological potential [66]. Over the past decade, five new spirotetronate compounds active against Gram-positive bacteria have been discovered (Table 2). Among them, lobophorin L (Figure 6), isolated from the marine-derived Streptomyces sp. 4506, displayed strong to moderate antibacterial activity against M. luteus and Bacillus thuringiensis, with MIC values ranging from 4 to 8 μg/mL (Table 2) [53]. SAR insights indicate that the degree of sugar substitution at C-9 correlates positively with antibacterial The two sugar moiety substitution in lobophorin L (MIC of 8 μg/mL) showed the strongest antibacterial activity compared with lobophorin M (one sugar moiety substitution, with MIC above 128 μg/mL) against M. luteus [53]. Using the CRISPR-Cas9 gene cluster activation strategy, Lim et al. [54] reported the discovery of a novel doubly glycosylated 24-membered polyene macrolactam, named auroramycin, from a silent BGC in S. roseosporus NRRL 15998 (Figure 6). Auroramycin showed potent antibacterial activity against MRSA with MICs of 1–2 μg/mL. It also inhibited other Gram-positive pathogenic bacteria such as S. aureus (vancomycin-intermediate (VI) MRSA) and vancomycin-resistant* E. faecalis* (VRE) with MICs ranging from 1 to 4 μg/mL (Table 2).
As shown in Table 3, 12 additional compounds belonging to different classes of polyketides have been reported within the Streptomyces genus over the last decade, with half of them displaying negligible inhibitory effect (MIC > 100* μ*g/mL) against Gram-positive bacteria.
There have been 71 natural peptide antibiotic products derived from Streptomyces, known for their biological activity against Gram-positive bacteria, since 2013. Fifty-two of these peptides are cyclic peptides and cyclic peptides containing piperazic acid (Table 4).
Among the cyclic peptides identified, actinomycins emerged as the most potent cyclic peptides exhibiting significant inhibitory activity against Gram-positive bacteria. These compounds, isolated from various Streptomyces species, are well-known chromopeptides consisting of two cyclic pentapeptide lactones (α- and β-rings) attached through amide bonds to a central phenoxazinone chromophore [87].
Over the past decade, several natural actinomycins have been described, notably those classified as D-type actinomycins. Among them, actinomycins D1–D4, derived from the fermentation broth of a strain of marine sponge-associated Streptomyces sp. LHW52447, demonstrated remarkable activity against Gram-positive bacteria (Figure 7). Specifically, actinomycins D1 and D2 exhibited potent antibacterial activity against MRSA (strain ATCC 33591), with MIC values ranging from 0.125 to 0.25 μg/mL, compared to D3 and D4, which showed MIC values between 0.5 and 1.0 μg/mL (Table 4) [70]. The enhanced activity of D1 and D2 suggests that the presence of an additional oxazole ring in the phenoxazinone chromophore markedly boosts anti-MRSA efficacy [70].
Additionally, ilamycins, also referred to as rufomycins, constitute a significant family of cycloheptapeptides for their antibacterial properties against Gram-positive bacteria (Figure 7). During antituberculosis drug discovery efforts, 12 new ilamycins were isolated from a large-scale (200 L) fermentation of the mutant strain S. atratus SCSIO ZH16 ΔilaR. These compounds demonstrated potent antitubercular activity against Mycobacterium tuberculosis H37Rv, with MIC values ranging from 0.001 to 1.058 μg/mL (0.0096–10 μM) (Table 4) [71]. SAR data point to two important cyclization at C-33 improves the antitubercular activity of ilamycins significantly, and the C-43 nitro group appears to play a key role in determining antitubercular activity [71].
Another potent anti-M. tuberculosis H37Rv rufomycin, rufomycin 58, was isolated from S. atratus strain MJM3502. It strongly inhibited this bacterium, with an MIC value of just 0.0088 μg/mL (0.0085 μM) (Table 4) [72]. It was concluded that the new in-chain cyclic 2-pyrrolidinone, in rufomycin 58, was linked to its potent anti-M. tuberculosis activity, comparable to or greater than that of the 2-piperidinone structures [72].
Lunaemycin A, a cyclic hexapeptide, was successfully isolated from the cave moonmilk-derived S. lunaelactis MM109T (Figure 7). It demonstrated efficacy in inhibiting a panel of bacteria, including B. subtilis ATCC 6633, Streptococcus pyogenes ATCC 12344, S. aureus (ATCC 25923 and ATCC 43300), Staphylococcus epidermidis SI-1266, Staphylococcus haemolyticus SI-6/2011, Staphylococcus warneri SI-5/2011, E. faecalis (ATCC 29212 and SI-759), and E. faecium SI-1831, with MICs of 0.12 and 0.25 μg/mL (Table 4) [73].
Among the 15 identified lipopeptides, ambocidins A and B have emerged as the most potent, exhibiting significant inhibitory activity against Gram-positive bacteria (Figure 8 and Table 5). These compounds, identified as calcium-dependent lipodepsipeptides, were induced and isolated by cloning a silent BGC (the amb cluster) from S. ambofaciens ATCC 2387 and integrating it into the chromosome of S. avermitilis. Ambocidins A and B strongly inhibited B. subtilis E168 with an MIC value below 0.031 μg/mL. Against other Gram-positive bacteria (S. aureus and E. faecium), ambocidin A remains the most active, with MIC values ranging from 0.25 to only 1 μg/mL [88]. SAR observations reveal that both the fatty acid chain length and hydroxylation of Arg^7^ have a significant effect on activity, with ambocidin A emerging as the most effective congener [88].
Gausemycins A and B, two additional potent lipopeptides, were purified from Streptomyces sp. INA-Ac-5812 (Figure 8). These lipoglycopeptides exhibited strong antistaphylococcal activity against S. aureus ATCC 29213, S. aureus ATCC 33592 (MRSA), and S. epidermidis ATCC 14990, with MICs ranging from 0.25 to 1 μg/mL and remained moderately to weakly active against other Gram-positive bacteria (Table 5) [89].
Over the past decade, five RiPPs inhibiting exclusively Gram-positive bacteria have been identified, among which globimycin and sviceucin stand out as the most potent, demonstrating remarkable inhibitory activity (Table 6).
Globimycin, a thiopeptide, was discovered through genome mining from the extract of S. globisporus subsp. globisporus (Figure 9). This peptide exhibits strong antibacterial activity against B. subtilis, S. aureus, and M. luteus, with MIC values ranging from 0.25 to 1 μg/mL (Table 6) [96].
Sviceucin, a lasso peptide, was isolated from the culture broth of S. sviceus (Figure 9). It selectively targets Gram-positive bacteria, including Bacillus megaterium, Lactobacillus bulgaricus 340, S. aureus subsp. aureus ATCC 6538, and L. sakei subsp. sakei DSM 20017, with MIC values ranging from 1.3 to 2.6 μg/mL (1.25–2.5 μM). Additionally, sviceucin was shown to inhibit fsr quorum sensing in E. faecalis (Table 6) [97].
As shown in Table 7, 23 terpenoids, displaying antibacterial activity against Gram-positive bacteria, from Streptomyces have been isolated over the past decade. These compounds, although generally less effective than previously discovered compounds, include notable exceptions with significant antibacterial activity. Among them, napyradiomycin 2, belonging to the meroterpenoid class, stands out (Figure 10). Isolated from the culture broth of a marine-derived actinomycete (Streptomyces sp. SCSIO 10428), this compound exhibited significant antibacterial activity against S. aureus ATCC 29213, B. subtilis SCSIO BS01, and B. thuringiensis SCSIO BT01, with MIC values of 0.5, 1, and 1 μg/mL, respectively (Table 7) [101]. Belonging to the same class of meroterpenoids, the newly identified merochlorin I exhibits potent antibacterial activity (Figure 10). It was purified, along with three other merochlorins, from the liquid culture of Streptomyces sp. CNH-189, a strain isolated from a marine sediment. Merochlorin I demonstrated significant antibacterial effect against B. subtilis KCTC 1021, K. rhizophila KCTC 1915, and S. aureus KCTC 1927, with MIC values of 1, 2, and 2 μg/mL, respectively (Table 7) [102]. It is important to point out that the presence of a polar moiety at the isoprene chain (C-19) abolishes the antibacterial properties of merochlorins, which was shown with the hydroxy group in merochlorin H and the amine group in merochlorin J [102].
Additionally, chemical investigation of the ethyl acetate extract from the marine-derived S. griseorubens led to the discovery of five new labdane-type diterpenoids. Among them, chlorolabdan B exhibited significant activity, with MIC values ranging from 4 to 8 μg/mL against B. subtilis KCTC 102, M. luteus KCTC 1915, and S. aureus KCTC 1927 (Table 7 and Figure 10) [103].
Naphthoquinone-based meroterpenoids are a class of hybrid natural products derived from polyketide and terpenoid biosynthetic pathways. Since 2013, only five compounds have been isolated with exclusive activity against Gram-positive bacteria (Table 8). Among them, flaviogeranin D demonstrated significant antibacterial activity, with MIC values of 5.2 μg/mL against Mycobacterium smegmatis MC^2^ 255 and 9.2 μg/mL against S. aureus ATCC 43300 (Table 8 and Figure 11) [107]. Unlike its analogues (flaviogeranin B1 and flaviogeranin B) bearing an amine at C-8, the absence of this group in flaviogeranin D correlates with increased activity [107].
Among six alkaloids described, three of them stand out as the most potent, demonstrating remarkable inhibitory activity (Table 9). The first ones are streptopyrroles B and C, which were isolated from the marine-derived actinomycete, strain S. zhaozhouensis 208DD-064 (Figure 12). These pyrrole-containing alkaloids showed significant activity against B. subtilis KCTC 1021, M. luteus KCTC 1915, and S. aureus KCTC 1927 with MIC values ranging from 0.23 to 0.98 μg/mL (0.7–2.9 μM) (Table 9) [109]. Against B. subtilis KCTC 1021, streptopyrrole B is more potent (MIC: 0.26 μg/mL [0.8 μM]) than streptopyrrole C (MIC: 0.98 μg/mL [2.9 μM]). SAR suggests that monochloride substitution (streptopyrrole B) enhances potency compared to dichloride substitution (streptopyrrole C) [109]. The second one is dionemycin, a chlorinated bis-indole alkaloid obtained from deep-sea derived Streptomyces sp. SCSIO 11791 (Figure 12). It shows antistaphylococcal activity with an MIC range of 1–2 μg/mL against clinic strains of MRSA and an MIC of 0.5 μg/mL against M. luteus ML01 Ju1 (Table 9) [110]. The chlorine at C-6^″^, in dionemycin, appears essential for increased antibacterial activity in contrast to similar analogues lacking this substitution [110].
We present below four new phenazine metabolites discovered in the last decade exhibiting exclusive activity against Gram-positive bacteria (Table 10).
The compounds phenazine SC and hydroxy-7-oxolavanducyanin have emerged as highly potent phenazines with remarkable inhibitory activity (Figure 13). Phenazine SC, derived from Streptomyces sp. (strain NA04227) associated with an earwig, demonstrated strong activity against M. luteus, with an MIC of 1.48 μg/mL (Table 10) [112]. Its antibacterial strength is attributed to the presence of a geranyl group, which is not found in other related phenazine derivatives (SA and SB) [112].
Hydroxy-7-oxolavanducyanin, an analogue of lavanducyanin, was isolated from a soil-derived actinomycete (Streptomyces sp. CPCC 203577) (Figure 13). It exhibited significant activity against S. epidermidis ATCC 12228 (MSSE), S. aureus ATCC 29213 (MSSA), and S. aureus ATCC 33591, with MIC values of 0.06, 8, and 8 μg/mL, respectively (Table 10) [113].
Among 11 nucleoside antibiotics described, mavintramycins A and F demonstrate remarkable inhibitory activity (Table 11 and Figure 14). Mavintramycins A and F, isolated from the culture broth of Streptomyces sp. OPMA40551, were identified as active compounds against the Mycobacterium avium complex, specifically targeting both M. avium and Mycobacterium intracellulare (Figure 14). These compounds exhibited the most potent and selective inhibitory activity among the tested compounds, with MIC values ranging from 0.39 to 3.12 μg/mL for mavintramycin A and 0.78–3.12 μg/mL for mavintramycin F (Table 11) [116].
Over the past decade, 19 other novel compounds produced by Streptomyces species, specifically exhibiting activity against Gram-positive bacteria, have been identified (Table 12). These compounds belong to distinct chemical classes, with approximately 30% demonstrating moderate to weak activity depending on the target strain.
In the years between 1940 and 1960, a period known as the golden age of antibiotic discovery, 20 new classes of antibiotics have been developed. However, with the beginning of the 21st century, only two new classes were oxazolidin-2-ones and daptomycin [129, 130]. Most of the antibiotics discovered during the antibiotic golden age are still used clinically, but their efficacy has been reduced by the emergence of multidrug-resistant bacteria [129, 131]. Among the problematic bacterial strains are Gram-positive bacteria such as S. aureus, E. faecium, Streptococcus pneumoniae, and M. tuberculosis [132]. The increasing reports of these strains resistant to first-line drugs [133] show that it is essential to develop new antibacterial compounds with core structures significantly different from those of the previous generation of antibiotics.
Over the past decade, Streptomyces-derived compounds have attracted increasing interest due to their notable bioactivity against Gram-positive bacteria, including antibiotic-resistant strains such as MRSA and VRE. This review highlighted 248 newly identified molecules, isolated from Streptomyces species or strains, belonging to different chemical classes. The polyketides and peptides are emerging as the most productive in terms of quantity and activity. This can be explained by the fact that between half and three-quarters of the BGCs in the Streptomyces genus encode enzyme complexes, such as NRPSs and PKSs, and their hybrid compounds [9].
Building on this molecular diversity, it is crucial to explore in more detail the biosynthetic mechanisms that allow Streptomyces to produce such structurally and functionally diverse substances. Among the compounds exhibiting considerable bioactivity, recent studies have elucidated or predicted biosynthetic pathways that highlight the metabolic flexibility of Streptomyces. Formicamycins, which are strong antibacterial aromatic polyketides derived from S. formicae, are produced through a type II PKS system. This pathway involves ketosynthases and cyclases that mediate the formation of aromatic polyketide scaffolds. Importantly, several enzymes that modify the structures post-PKS, such as halogenases and oxygenases, contribute to the structural diversity observed in formicamycins and fasamycins. The regulation of this BGC is carefully controlled by various transcription factors, making it a model for exploring the regulation of antibiotic production [32].
Ilamycins, also known as rufomycins, are complex cyclic peptides produced by bacteria using a specific biosynthetic pathway. A prenyltransferase enzyme modifies tryptophan by adding a prenyl group, resulting in the prenylated tryptophan that is part of the final molecule. Another key part of the pathway is a nitric oxide synthase (NOS) and a cytochrome P450 enzyme known as RufO. The NOS produces nitric oxide, and RufO uses this to nitrate tyrosine, forming 3-nitrotyrosine. This modified tyrosine is subsequently incorporated into the peptide by the NRPS. Once the ring is assembled, additional modifying enzymes, including other P450s, make further chemical transformations to complete the biosynthesis of ilamycins. This pathway enables bacteria, such as Streptomyces, to produce a range of biologically active compounds with strong antituberculosis properties [134]. These comprehensive biosynthetic insights not only highlight the enzymatic capacity of Streptomyces but also emphasize the link between metabolic pathways and their end-products.
Furthermore, SAR studies revealed critical insights about the structural features that affect the antibacterial effectiveness of newly identified Streptomyces-derived compounds. For instance, the patterns of halogenation, including the presence and type of halogen atoms (e.g., chlorine compared to bromine) in formicamycins and streptopyrroles, significantly influenced their antibacterial activity. Similarly, functional groups such as the 5-O-methyl in streptovertimycin G, or the oxazole ring in actinomycins D1 and D2, were found to boost activity when compared to their analogues (actinomycins D3 and D4). The importance of particular groups, such as the C-43 nitro group in ilamycins, the methyl group at C-2 in anthracimycin, and sugar substitutions at C-9 in lobophorins, were all identified as key factors for bioactivity. These insights into the SAR of Streptomyces-derived metabolites pave the way for a more detailed investigation of certain compounds, which not only dominate in their varied structures but also show remarkable antibacterial potency.
Focusing more specifically on polyketides, the aromatic subclass stands out not only as the most dominant but also as one of the most potent. Compounds such as cervinomycins and kebanmycins have demonstrated interestingly low MIC values (0.008 μg/mL for cervinomycins B4 against S. aureus 16-30 [MRSA]) (Table 1). Cervinomycins B1–B4 are more efficient than cervinomycins A1 and A2, which were first isolated by S. cervinus sp. nov. [135] underlining their future therapeutic potential. In addition to these compounds, anthracimycin stands out as another powerful polyketide belonging to the macrolide subclass with a low minimum MIC value of 0.031 μg/mL against B. anthracis (strain UM23C1-1) and other Gram-positive bacteria including S. aureus ATCC 13709 and E. faecalis ATCC 29212 (MICs: 0.0625–0.125 μg/mL) (Table 2) [51]. While the majority of macrolide antibiotics act by targeting the 50S ribosomal subunit to block protein synthesis [136], it has been suggested that anthracimycin exhibits its bactericidal activity by inhibiting DNA and/or RNA synthesis in the absence of DNA intercalation [137]. Anthracimycin's high antibacterial potency, novel molecular structure, and new mechanism of action make it a target of choice for the development of new antibiotics [138].
Peptide-based antibiotics, notably actinomycins D1–D4 and ilamycins, possess strong anti-Gram-positive bacteria activity (Table 4). Actinomycins D1–D4 are structurally similar to actinomycin D, also called dactinomycin, which was the first antibiotic compound shown to have anticancer activity [87]. There are generally some structural differences between actinomycin compounds, which contribute to improving their antimicrobial profiles, confirming that actinomycins D1–D4 would probably be promising candidates for drug development, although further information on toxicity is required. Ilamycins also showed especial antituberculosis activity, such as rufomycin 58 with an MIC of just 0.0088 μg/mL (Table 4). This suggests that certain peptide antibiotics may have dual activity against both common and mycobacterial pathogens. Previous studies have shown that ilamycins exert their antimycobacterial activity by inhibiting the proteolytic activity of the ClpC1/P1/P2 complex, a critical component involved in regulated protein degradation in M. tuberculosis [139].
In addition to these compounds, the recently discovered lipodepsipeptides ambocidins A and B have shown to be particularly effective as peptide-based antibiotics. These calcium-dependent cyclic lipopeptides demonstrated strong antibacterial activity against Gram-positive bacteria, with MIC values below 0.031 μg/mL against B. subtilis E168 and MICs ranging from 0.25 to 1 μg/mL against S. aureus and E. faecium (Table 5) [88]. In terms of their mode of action, ambocidins act by inhibiting bacterial cell wall biosynthesis through specific targeting of lipid II, a key precursor in the peptidoglycan synthesis pathway. Importantly, unlike vancomycin, ambocidins bind to a different site on lipid II, rather than relying on the D-Ala-D-Ala motif. This unique interaction was evidenced by their retained activity against VREfm and the failure of a D-Ala-D-Ala mimic to inhibit their activity [88]. These findings position ambocidins as promising candidates for the treatment of drug-resistant Gram-positive bacteria due to their strong activity and novel mechanism of action.
Despite terpenoids being less numerous, certain compounds such as napyradiomycin 2 and merochlorin I have demonstrated important antibacterial activity (MICs: 0.5–2 μg/mL) (Table 7) [101, 102]. Historically, Streptomyces has been viewed as a limited source of terpenoids (with the exception of geosmin) [26]. However, recent findings suggest an untouched biosynthetic potential that could be revealed by genome exploration and the activation of silent gene clusters.
Although other classes such as alkaloids, phenazines, and nucleoside antibiotics may be numerically underrepresented, they contain compounds of significant potency. For example, streptopyrroles (A and B) and dionemycin, both alkaloids, displayed MICs below 2 μg/mL (Table 9), highlighting the valuable bioactivity contributed by these less abundant chemical classes. Similarly, nucleoside antibiotics show significant antimicrobial potential, as highlighted by mavintramycin A (Table 11). This compound was discovered to be effective against the M. avium complex, specifically targeting both M. avium and M. intracellulare. When examining its main mode of action, mavintramycin A completely inhibited protein synthesis and strongly inhibited DNA synthesis in M. smegmatis, while it had very weak effects on RNA and peptidoglycan syntheses. Mavintramycin A was considered to bind to a distinct site on the ribosome compared to the commonly used clarithromycin and amikacin, corroborating the finding that no cross-resistant M. avium strains with this compound were identified [116].
In this systematic review, the majority of isolated compounds were mainly derived from marine environments (e.g., deep-sea sediments) and soil. This result is in line with the studies by Lacey and Rutledge [16] and Donald et al. [140]. This reinforces the idea that extreme ecosystems, like marine environments, are promising reservoirs of novel bioactive metabolites, possibly due to evolutionary pressure for chemical defense. Additionally, approximately 23% of these active compounds exhibited a range of additional bioactivities, including cytotoxic, antiviral, and neuroactive effects. This multifunctionality implies the presence of structural scaffolds with pharmacological versatility, potentially amenable to optimization for dual therapeutic uses.
Despite the promising, in vitro, antibacterial activity of the 248 reported compounds, only a small few (n = 5) have progressed to in vivo experiments, such as mavintramycin A, anthracimycin, and three liposidomycin congeners. These compounds have proven to be effective in animal models, particularly against infections caused by M. avium complex and B. anthracis.
In conclusion, this analysis underscores the significant role of Streptomyces as a rich source of structurally diverse and biologically potent compounds effective against Gram-positive bacteria. These compounds hold the potential to be developed into effective drugs to combat antibacterial resistance. The study also emphasizes the necessity of further exploring underrepresented environments and leveraging modern genetic tools to uncover hidden biosynthetic pathways.
The present systematic review has certain limitations. Firstly, out of the total selected articles, 20 could not be analyzed due to restricted access. In addition, several publications were excluded because they reported antibacterial activity using noncomparable metrics, such as DIZ, IC50, MIC50, MIC90, or MIC99, instead of standardized MIC values. This made it more difficult to select and present the most potent compounds. Despite these limitations, the defined inclusion and exclusion criteria, along with the consistent application of MIC-based potency assessments, contributed to a representative synthesis of the most promising compounds derived from the Streptomyces genus.
This systematic review summarizes Streptomyces anti-Gram-positive bacteria compounds reported in the last decade. The Streptomyces species/strains investigated originate from a wide range of biotopes, with marine sources being the most explored, followed by terrestrial soil. The recent investigations and efforts have led to the discovery of a total of 248 secondary metabolites representing diverse chemical classes, including polyketides, peptides, terpenoids, phenazines, and other natural products. The major ones are polyketides and peptides, representing 40.32% and 29.03% of the identified compounds. These discoveries show that Streptomyces remains an unexpectedly resource of structurally diverse natural products that can be developed into pharmaceutical drugs and, therefore, reduce multidrug resistance in Gram-positive bacteria, which poses a serious threat to human health.