Peptidoglycan types of bacterial cell walls and their taxonomic implications

Structural and kinetic analysis of the monofunctional Staphylococcus aureus PBP1

Staphylococcus aureus, an ESKAPE pathogen, is a major clinical concern due to its pathogenicity and manifold antimicrobial resistance mechanisms. The commonly used β-lactam antibiotics target bacterial penicillin-binding proteins (PBPs) and inhibit crosslinking of peptidoglycan strands that comprise the bacterial cell wall mesh, initiating a cascade of effects leading to bacterial cell death. S. aureus PBP1 is involved in synthesis of the bacterial cell wall during division and its presence is essential for survival of both antibiotic susceptible and resistant S. aureus strains. Here, we present X-ray crystallographic data for S. aureus PBP1 in its apo form as well as acyl-enzyme structures with distinct classes of β-lactam antibiotics representing the penicillins, carbapenems, and cephalosporins, respectively: oxacillin, ertapenem and cephalexin. Our structural data suggest that the PBP1 active site is readily accessible for substrate, with little conformational change in key structural elements required for its covalent acylation of β-lactam inhibitors. Stopped-flow kinetic analysis and gel-based competition assays support the structural observations, with even the weakest performing β-lactams still having comparatively high acylation rates and affinities for PBP1. Our structural and kinetic analysis sheds insight into the ligand-PBP interactions that drive antibiotic efficacy against these historically useful antimicrobial targets and expands on current knowledge for future drug design and treatment of S. aureus infections.

Leucobacter edaphi sp. nov., a highly chromate-tolerant bacterium isolated from chromium containing chemical plant soil

A Gram-positive, aerobic, rod-shaped non-motile, non-sporulating bacterium, designated CSA2T, was isolated from chromium-containing soils collected from a chemical plant. The 16S rRNA gene sequence of strain CSA2T showed the highest homology with Leucobacter chromiireducens subsp. solipictus (97.85%), Leucobacter chromiireducens subsp. chromiireducens (97.85%). The digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and the amino acid identity (AAI) values among strains CSA2T and the selected Leucobacter species were 20.6-23.4% (dDDH), 72.67-78.03% (ANI) and 66.39-76.16% (AAI), falling below the recommended thresholds for species delimitation. The principal fatty acids were anteiso-C15:0, iso-C16:0 and anteiso-C17:0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The major menaquinones detected were MK-10 and MK-11. The cell-wall amino acids included 2,4-diaminobutyric acid, threonine, glutamic acid, alanine and glycine. Based on molecular feature, phenotypic and chemotaxonomic, strain CSA2T was considered to be a novel species of the genus Leucobacter., and the name Leucobacter edaphi sp. nov. is proposed. The type strain is CSA2T (= JCM 34360T = CGMCC 1.18747T).

Streptomyces changanensis sp. nov. Isolated from Soil in China

An aerobic, Gram-positive, and non-motile actinomycete, designated HL-66 T, was isolated from a soil sample collected in the Meridian Valley, Shaanxi Province, China. Morphological, chemotaxonomic, and phylogenetic characteristics showed a high similarity to the genus Streptomyces. Based on 16S rRNA gene sequence analysis, the closest phylogenetic neighbour of HL-66 T were Streptomyces lavendofoliae NBRC 12882 T (99.17%), Streptomyces gobitricini NBRC 15419 T (99.03%) and Streptomyces roseolilacinus NBRC 12815 T (98.96%). Genome relatedness indexes revealed that the average nucleotide identity and digital DNA-DNA hybridization values between HL-66 T and its closest phylogenomic relative (S. roseolilacinus JCM 4335 T) were 88.61% and 32.10%, respectively. The cell-wall peptidoglycan contains LL-diaminopimelic acid. Predominant menaquinones are MK-9 (H6), MK-9(H4) and MK-9(H8). The major cellular fatty acids were iso-C16:0, anteiso-C15:0, iso-C16:1 H, and C16:1 ω7c. The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, and an unknown phospholipid. Based on phylogenetic analyses, genome-genome distance calculation, and average nucleotide identity, strain HL-66 T represents a novel species of the genus Streptomyces. Therefore, a new species Streptomyces changanensis sp. nov. is proposed with strain HL-66 T (= CGMCC 22674 = JCM 35800) as the type strain.

Spatial and temporal localization of cell wall associated pili in Enterococcus faecalis

Enterococcus faecalis virulence requires cell wall-associated proteins, including the sortase-assembled endocarditis and biofilm associated pilus (Ebp), important for biofilm formation in vitro and in vivo. The current paradigm for sortase-assembled pilus biogenesis in Gram-positive bacteria is that sortases attach substrates to lipid II peptidoglycan (PG) precursors, prior to their incorporation into the growing cell wall. Contrary to prevailing dogma, by following the distribution of Ebp and PG throughout the E. faecalis cell cycle, we found that cell surface Ebp do not co-localize with newly synthesized PG. Instead, surface-exposed Ebp are localized to the older cell hemisphere and excluded from sites of new PG synthesis at the septum. Moreover, Ebp deposition on the younger hemisphere of the E. faecalis diplococcus appear as foci adjacent to the nascent septum. We propose a new model whereby sortase substrate deposition can occur on older PG rather than at sites of new cell wall synthesis. Consistent with this model, we demonstrate that sequestering lipid II to block PG synthesis via ramoplanin, does not impact new Ebp deposition at the cell surface. These data support an alternative paradigm for sortase substrate deposition in E. faecalis, in which Ebp are anchored directly onto uncrosslinked cell wall, independent of new PG synthesis.

Structure Activity Relationship of the Stem Peptide in Sortase A Mediated Ligation from Staphylococcus aureus

The surfaces of most Gram-positive bacterial cells, including that of Staphylococcus aureus (S. aureus), are heavily decorated with proteins that coordinate cellular interactions with the extracellular space. In S. aureus, sortase A is the principal enzyme responsible for covalently anchoring proteins, which display the sorting signal LPXTG, onto the peptidoglycan (PG) matrix. Considerable efforts have been made to understand the role of this signal peptide in the sortase-mediated reaction. In contrast, much less is known about how the primary structure of the other substrate involved in the reaction (PG stem peptide) could impact sortase activity. To assess the sortase activity, a library of synthetic analogs of the stem peptide that mimic naturally existing variations found in the S. aureus PG primary sequence were evaluated. Using a combination of two unique assays, we showed that there is broad tolerability of substrate variations that are effectively processed by sortase A. While some of these stem peptide derivatives are naturally found in mature PG, they are not known to be present in the PG precursor, lipid II. These results suggest that sortase A could process both lipid II and mature PG as acyl-acceptor strands that might reside near the membrane, which has not been previously described.

Streptomyces tsukubensis VKM Aс-2618D-an Effective Producer of Tacrolimus

The Streptomyces sp. VKM Ac-2618D strain has been identified, and its morphological and physiological features have been studied in relation to the production of the immunosuppressant tacrolimus. The phenotypic variability of the strain was analyzed, and a dissociant with a high level of tacrolimus production was selected. Based on a comprehensive study of morphological, physiological, and chemotaxonomic properties and on phylogenetic analysis, the strain was named Streptomyces tsukubensis VKM Ac-2618D. The strain genome contains the full version of the tacrolimus biosynthetic gene cluster. The advantages of fed-batch cultivation mode for tacrolimus biosynthesis are shown. The results broaden the understanding of the characteristics of polyketide biosynthesis and can be used in the development of technology for tacrolimus production.

Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter

Strain MD1^T is an anaerobic, Gram-stain-negative bacterium isolated from a lab-scale biogas fermenter fed with maize silage. It has a rod-shaped morphology with peritrichously arranged appendages and forms long chains of cells and coccoid structures. The colonies of MD1^T were white, circular, slightly convex and had a smooth rim. The isolate is mesophilic, displaying growth between 25 and 45 °C with an optimum at 40 °C. It grew at pH values of pH 6.7-8.2 (optimum, pH 7.1) and tolerated the addition of up to 1.5% (w/v) NaCl to the medium. The main cellular fatty acids of MD1^T are C_14:0 DMA and C_16:0. Strain MD1^T fermented xylose, arabinose, glucose, galactose, cellobiose, maltose, maltodextrin10, lactose starch, and xylan, producing mainly 2-propanol and acetic acid. The genome of the organism has a total length of 4163427 bp with a G+C content of 38.5 mol%. The two closest relatives to MD1^T are Mobilitalea sibirica P3M-3^T and Anaerotaenia torta FH052^T with 96.44 or 95.8 % 16S rRNA gene sequence similarity and POCP values of 46.58 and 50.58%, respectively. As MD1^T showed saccharolytic and xylanolytic properties, it may play an important role in the biogas fermentation process. Closely related variants of MD1^T were also abundant in microbial communities involved in methanogenic fermentation. Based on morphological, phylogenetic and genomic data, the isolated strain can be considered as representing a novel genus in the family Lachnospiraceae, for which the name Variimorphobacter saccharofermentans gen. nov., sp. nov. (type strain MD1^T=DSM 110715^T=JCM 39125^T) is proposed.

MagC is a NplC/P60-like member of the α-2-macroglobulin Mag complex of Pseudomonas aeruginosa that interacts with peptidoglycan

Bacterial α-2 macroglobulins (A2Ms) structurally resemble the large spectrum protease inhibitors of the eukaryotic immune system. In Pseudomonas aeruginosa, MagD acts as an A2M and is expressed within a six-gene operon encoding the MagA-F proteins. In this work, we employ isothermal calorimetry (ITC), analytical ultracentrifugation (AUC), and X-ray crystallography to investigate the function of MagC and show that MagC associates with the macroglobulin complex and with the peptidoglycan (PG). However, the catalytic residues of MagC display an inactive conformation that could suggest that it binds to PG but does not degrade it. We hypothesize that MagC could serve as an anchor between the MagD macroglobulin and the PG and could provide stabilization and/or regulation for the entire complex.

Engineered Sortases in Peptide and Protein Chemistry

The transpeptidase sortase A of Staphylococcus aureus (Sa-SrtA) is a valuable tool in protein chemistry. The native enzyme anchors surface proteins containing a highly conserved LPxTG sorting motif to a terminal glycine residue of the peptidoglycan layer in Gram-positive bacteria. This reaction is exploited for sortase-mediated ligation (SML), allowing the site-specific linkage of synthetic peptides and recombinant proteins by a native peptide bond. However, the moderate catalytic efficiency and specificity of Sa-SrtA fueled the development of new biocatalysts for SML, including the screening of sortase A variants form microorganisms other than S. aureus and the directed protein evolution of the Sa-SrtA enzyme itself. Novel display platforms and screening formats were developed to isolate sortases with altered properties from mutant libraries. This yielded sortases with strongly enhanced catalytic activity and enzymes recognizing new sorting motifs as substrates. This minireview focuses on recent advances in the field of directed sortase evolution and applications of these tailor-made enzymes in biochemistry.

Structure-function analysis of PGRP-S1 from the oriental armyworm, Mythimna separata

Peptidoglycan recognition proteins (PGRPs) are well known for their abilities to recognize or hydrolyze peptidoglycan (PGN), one of the major bacterial cell wall components. However, much less is known about their antifungal activities. PGRP-S1 was previously identified from a crop pest, Mythimna separata (Walker) (Lepidoptera: Noctuidae). PGRP-S1 showed bacteriolytic activities against Gram-positive and Gram-negative bacteria. In this study, tissue expression analysis showed that PGRP-S1 was mainly expressed in the midgut of naïve larvae. The induction analysis showed that it was significantly induced in the larval midgut 12 h post the injection of Beauveria bassiana conidia. To identify the key residues that are related to its microbicidal activities, the structure of PGPR-S1 was predicted for structural comparison and molecular docking analysis. Six residues (H61, H62, Y97, H171, T175, and C179) were mutated to Ala individually by site-directed mutagenesis. The recombinant wild-type (WT) and mutant proteins were expressed and purified. The recombinant proteins bound to different polysaccharides, PGNs, and bacteria. H61A, Y97A, H171A, and C179A lost amidase activity. Accordingly, antibacterial assay and scanning electron microscopy confirmed that only H62A and T175A retained bacteriolytic activities. The germination of B. bassiana conidia was significantly inhibited by WT, H61A, Y97A, T175A, and C179A mutants. Electron microscopy showed that some conidia became ruptured after treatment. The growth of hyphae was inhibited by the WT, H61A, H62A, and T175A. In summary, our data showed that different residues of PGRP-S1 are involved in the antibacterial and antifungal activities.

Synthesis of Carbapenems Containing Peptidoglycan Mimetics and Inhibition of the Cross-Linking Activity of a Transpeptidase of l,d Specificity

The carbapenem class of β-lactams has been optimized against Gram-negative bacteria producing extended-spectrum β-lactamases by introducing substituents at position C2. Carbapenems are currently investigated for the treatment of tuberculosis as these drugs are potent covalent inhibitors of l,d-transpeptidases involved in mycobacterial cell wall assembly. The optimization of carbapenems for inactivation of these unusual targets is sought herein by exploiting the nucleophilicity of the C8 hydroxyl group to introduce chemical diversity. As β-lactams are structure analogs of peptidoglycan precursors, the substituents were chosen to increase similarity between the drug and the substrate. Fourteen peptido-carbapenems were efficiently synthesized. They were more effective than the reference drug, meropenem, owing to the positive impact of a phenethylthio substituent introduced at position C2 but the peptidomimetics added at position C8 did not further improve the activity. Thus, position C8 can be modified to modulate the pharmacokinetic properties of highly efficient carbapenems.

Agromyces kandeliae sp. nov., isolated from rhizosphere soil of Kandelia candel in a mangrove

A novel, Gram-stain-positive, aerobic, non-spore-forming, non-motile and irregular rod-shaped bacterium designated Q22^T was isolated from the rhizosphere soil of mangrove plant, Kandelia candel collected in Zhangzhou, Fujian province, China. Strain Q22^T was able to grow at 10-40 °C (optimum 30 °C), pH 5.5-9.0 (optimum 7.0-8.0) and with 0-5.0% (w/v) NaCl (optimum 1.0 %). The genomic DNA G+C content was 71.9%. The average nucleotide identity, and in silico DNA-DNA hybridization values between strain Q22^T and the reference strains were 79.7-88.9% and 22.6-37.4%, respectively. The predominant isoprenoid quinone was MK-12 and the major fatty acids were anteiso-C_15:0, iso-C_16:0 and anteiso-C_17:0. The major polar lipids of strain Q22^T were diphosphatidylglycerol, phosphatidylglycerol, one glycolipid and three unidentified lipids. The strain Q22^T contained 2,4-diaminobutyric acid, alanine acid, glutamic acid and glycine in the peptidoglycans. The phylogenetic analysis and genotypic features, along with the phenotypic and chemotaxonomic characteristics, indicate that strain Q22^T represents a novel species of the genus Agromyces, for which the name Agromyces kandeliae sp. nov. is proposed. The type strain is Q22^T (=MCCC 1K03340^T= KCTC 39961^T).

Competing Substrates for the Bifunctional Diaminopimelic Acid Epimerase/Glutamate Racemase Modulate Peptidoglycan Synthesis in Chlamydia trachomatis

The Chlamydia trachomatis genome encodes multiple bifunctional enzymes, such as DapF, which is capable of both diaminopimelic acid (DAP) epimerase and glutamate racemase activity. Our previous work demonstrated the bifunctional activity of chlamydial DapF in vitro and in a heterologous system (Escherichia coli). In the present study, we employed a substrate competition strategy to demonstrate DapF _Ct function in vivo in C. trachomatis We reasoned that, because DapF _Ct utilizes a shared substrate-binding site for both racemase and epimerase activities, only one activity can occur at a time. Therefore, an excess of one substrate relative to another must determine which activity is favored. We show that the addition of excess l-glutamate or meso-DAP (mDAP) to C. trachomatis resulted in 90% reduction in bacterial titers, compared to untreated controls. Excess l-glutamate reduced in vivo synthesis of mDAP by C. trachomatis to undetectable levels, thus confirming that excess racemase substrate led to inhibition of DapF _Ct DAP epimerase activity. We previously showed that expression of dapF_Ct in a murI (racemase) ΔdapF (epimerase) double mutant of E. coli rescues the d-glutamate auxotrophic defect. Addition of excess mDAP inhibited growth of this strain, but overexpression of dapF_Ct allowed the mutant to overcome growth inhibition. These results confirm that DapF _Ct is the primary target of these mDAP and l-glutamate treatments. Our findings demonstrate that suppression of either the glutamate racemase or epimerase activity of DapF compromises the growth of C. trachomatis Thus, a substrate competition strategy can be a useful tool for in vivo validation of an essential bifunctional enzyme.

Chemical Tools for Illumination of Tuberculosis Biology, Virulence Mechanisms, and Diagnosis

Tuberculosis (TB) remains one of the deadliest infectious diseases and begs the scientific community to up the ante for research and exploration of completely novel therapeutic avenues. Chemical biology-inspired design of tunable chemical tools has aided in clinical diagnosis, facilitated discovery of therapeutics, and begun to enable investigation of virulence mechanisms at the host-pathogen interface of Mycobacterium tuberculosis. This Perspective highlights chemical tools specific to mycobacterial proteins and the cell lipid envelope that have furnished rapid and selective diagnostic strategies and provided unprecedented insights into the function of the mycobacterial proteome and lipidome. We discuss chemical tools that have enabled elucidating otherwise intractable biological processes by leveraging the unique lipid and metabolite repertoire of mycobacterial species. Some of these probes represent exciting starting points with the potential to illuminate poorly understood aspects of mycobacterial pathogenesis, particularly the host membrane-pathogen interactions.

Tessaracoccus coleopterorum sp. nov., isolated from the intestine of the dark diving beetle, Hydrophilus acuminatus

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated as strain HDW20^T, isolated from the intestine of the dark diving beetle Hydrophilus acuminatus. The isolate was Gram-stain-positive, facultatively anaerobic, non-motile, coccus-shaped, and formed pale orange colonies. Phylogenetic analysis based on 16S rRNA gene sequences and genome sequences showed that the isolate belonged to the genus Tessaracoccus in the phylum Actinobacteria and was closely related to T. flavescens SST-39^T, T. defluvii JCM 17540^T, and T. aquimaris NSG39^T, with the highest 16S rRNA gene sequence similarity of 98.5 % and a highest average nucleotide identity (ANI) value of 80.6 %. The major cellular fatty acids were C_18 : 1  ω9c and anteiso-C_15 : 0. The main respiratory quinone was MK-9 (H₄). The major polar lipid components were phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 69.0 %. The isolate contains ʟʟ-diaminopimelic acid, ʟ-alanine, and ʟ-lysine as amino acid components, and ribose, glucose, and galactose as sugar components of the cell wall peptidoglycan. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggested that strain HDW20^T represents a novel species within the genus Tessaracoccus. We propose the name Tessaracoccus coleopterorum sp. nov. The type strain is HDW20^T (=KACC 21348^T=KCTC 49324^T=JCM 33674^T).

Engineered Lysins With Customized Lytic Activities Against Enterococci and Staphylococci

The emergence of multidrug-resistant bacteria has made minor bacterial infections incurable with many existing antibiotics. Lysins are phage-encoded peptidoglycan hydrolases that have demonstrated therapeutic potential as a novel class of antimicrobials. The modular architecture of lysins enables the functional domains – catalytic domain (CD) and cell wall binding domain (CBD) – to be shuffled to create novel lysins. The CD is classically thought to be only involved in peptidoglycan hydrolysis whereas the CBD dictates the lytic spectrum of a lysin. While there are many studies that extended the lytic spectrum of a lysin by domain swapping, few have managed to introduce species specificity in a chimeric lysin. In this work, we constructed two chimeric lysins by swapping the CBDs of two parent lysins with different lytic spectra against enterococci and staphylococci. We showed that these chimeric lysins exhibited customized lytic spectra distinct from the parent lysins. Notably, the chimeric lysin P10N-V12C, which comprises a narrow-spectrum CD fused with a broad-spectrum CBD, displayed species specificity not lysing Enterococcus faecium while targeting Enterococcus faecalis and staphylococci. Such species specificity can be attributed to the narrow-spectrum CD of the chimeric lysin. Using flow cytometry and confocal microscopy, we found that the E. faecium cells that were treated with P10N-V12C are less viable with compromised membranes yet remained morphologically intact. Our results suggest that while the CBD is a major determinant of the lytic spectrum of a lysin, the CD is also responsible in the composition of the final lytic spectrum, especially when it pertains to species-specificity.

Building peptidoglycan inside eukaryotic cells: A view from symbiotic and pathogenic bacteria

The peptidoglycan (PG), as the exoskeleton of most prokaryotes, maintains a defined shape and ensures cell integrity against the high internal turgor pressure. These important roles have attracted researchers to target PG metabolism in order to control bacterial infections. Most studies, however, have been performed in bacteria grown under laboratory conditions, leading to only a partial view on how the PG is synthetized in natural environments. As a case in point, PG metabolism and its regulation remain poorly understood in symbiotic and pathogenic bacteria living inside eukaryotic cells. This review focuses on the PG metabolism of intracellular bacteria, emphasizing the necessity of more in vivo studies involving the analysis of enzymes produced in the intracellular niche and the isolation of PG from bacteria residing within eukaryotic cells. The review also points to persistent infections caused by some intracellular bacterial pathogens and the extent at which the PG could contribute to establish such physiological state. Based on recent evidences, I speculate on the idea that certain structural features of the PG may facilitate attenuation of intracellular growth. Lastly, I discuss recent findings in endosymbionts supporting a cooperation between host and bacterial enzymes to assemble a mature PG.

Genetically Encoded Biosensor-Based Screening for Directed Bacteriophage T4 Lysozyme Evolution

Lysozyme is widely used as a model protein in studies of structure–function relationships. Recently, lysozyme has gained attention for use in accelerating the degradation of secondary sludge, which mainly consists of bacteria. However, a high-throughput screening system for lysozyme engineering has not been reported. Here, we present a lysozyme screening system using a genetically encoded biosensor. We first cloned bacteriophage T4 lysozyme (T4L) into a plasmid under control of the araBAD promoter. The plasmid was expressed in Escherichia coli with no toxic effects on growth. Next, we observed that increased soluble T4L expression decreased the fluorescence produced by the genetic enzyme screening system. To investigate T4L evolution based on this finding, we generated a T4L random mutation library, which was screened using the genetic enzyme screening system. Finally, we identified two T4L variants showing 1.4-fold enhanced lytic activity compared to native T4L. To our knowledge, this is the first report describing the use of a genetically encoded biosensor to investigate bacteriophage T4L evolution. Our approach can be used to investigate the evolution of other lysozymes, which will expand the applications of lysozyme.

Utilization of different MurNAc sources by the oral pathogen Tannerella forsythia and role of the inner membrane transporter AmpG

BACKGROUND

The Gram-negative oral pathogen Tannerella forsythia strictly depends on the external supply of the essential bacterial cell wall sugar N-acetylmuramic acid (MurNAc) for survival because of the lack of the common MurNAc biosynthesis enzymes MurA/MurB. The bacterium thrives in a polymicrobial biofilm consortium and, thus, it is plausible that it procures MurNAc from MurNAc-containing peptidoglycan (PGN) fragments (muropeptides) released from cohabiting bacteria during natural PGN turnover or cell death. There is indirect evidence that in T. forsythia, an AmpG-like permease (Tanf_08365) is involved in cytoplasmic muropeptide uptake. In E. coli, AmpG is specific for the import of N-acetylglucosamine (GlcNAc)-anhydroMurNAc(-peptides) which are common PGN turnover products, with the disaccharide portion as a minimal requirement. Currently, it is unclear which natural, complex MurNAc sources T. forsythia can utilize and which role AmpG plays therein.

RESULTS

We performed a screen of various putative MurNAc sources for T. forsythia mimicking the situation in the natural habitat and compared bacterial growth and cell morphology of the wild-type and a mutant lacking AmpG (T. forsythia ΔampG). We showed that supernatants of the oral biofilm bacteria Porphyromonas gingivalis and Fusobacterium nucleatum, and of E. coli ΔampG, as well as isolated PGN and defined PGN fragments obtained after enzymatic digestion, namely GlcNAc-anhydroMurNAc(-peptides) and GlcNAc-MurNAc(-peptides), could sustain growth of T. forsythia wild-type, while T. forsythia ΔampG suffered from growth inhibition. In supernatants of T. forsythia ΔampG, the presence of GlcNAc-anhMurNAc and, unexpectedly, also GlcNAc-MurNAc was revealed by tandem mass spectrometry analysis, indicating that both disaccharides are substrates of AmpG. The importance of AmpG in the utilization of PGN fragments as MurNAc source was substantiated by a significant ampG upregulation in T. forsythia cells cultivated with PGN, as determined by quantitative real-time PCR. Further, our results indicate that PGN-degrading amidase, lytic transglycosylase and muramidase activities in a T. forsythia cell extract are involved in PGN scavenging.

CONCLUSION

T. forsythia metabolizes intact PGN as well as muropeptides released from various bacteria and the bacterium's inner membrane transporter AmpG is essential for growth on these MurNAc sources, and, contrary to the situation in E. coli, imports both, GlcNAc-anhMurNAc and GlcNAc-MurNAc fragments.

Assembly of Peptidoglycan Fragments-A Synthetic Challenge

Peptidoglycan (PGN) is a major constituent of most bacterial cell walls that is recognized as a primary target of the innate immune system. The availability of pure PGN molecules has become key to different biological studies. This review aims to (1) provide an overview of PGN biosynthesis, focusing on the main biosynthetic intermediates; (2) focus on the challenges for chemical synthesis posed by the unique and complex structure of PGN; and (3) cover the synthetic routes of PGN fragments developed to date. The key difficulties in the synthesis of PGN molecules mainly involve stereoselective glycosylation involving NAG derivatives. The complex synthesis of the carbohydrate backbone commonly involves multistep sequences of chemical reactions to install the lactyl moiety at the O-3 position of NAG derivatives and to control enantioselective glycosylation. Recent advances are presented and synthetic routes are described according to the main strategy used: (i) based on the availability of starting materials such as glucosamine derivatives; (ii) based on a particular orthogonal synthesis; and (iii) based on the use of other natural biopolymers as raw materials.

Chryseoglobus indicus sp. nov., isolated from deep sea water

A novel Gram-stain-positive, motile, aerobic, non-spore-forming and slender rod-shaped actinobacterium, designated strain CTD02-10-2^T, was isolated from deep sea water of the Indian Ocean. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CTD02-10-2^T was grouped into a separated branch with Chryseoglobus frigidaquae JCM 14730^T (98.4 % nucleotide sequence identity). The respiratory quinones were menaquinones with 11, 12, 13 and 14 isoprene units and anteiso-C_15 : 0, iso-C_16 : 0, anteiso-C_15 : 1 A and anteiso-C_17 : 0 were the major fatty acids. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and three unknown glycolipids. The genome of strain CTD02-10-2^T was 2.59 Mb, with a DNA G+C content of 69.6 mol% and contained genes involved in the biosynthesis of alkylresorcinol, ansamycin, and carotenoids. In silico DNA-DNA hybridization and average nucleotide identity values for whole-genome sequence comparisons between strain CTD02-10-2^T and C. frigidaquae JCM 14730^T were clearly below the thresholds used for the delineation of a new species. Based on its morphological and chemotaxonomic characteristics, as well as genotypic data, strain CTD02-10-2^T was classified as a novel species of the genus Chryseoglobus, for which the name Chryseoglobus indicus sp. nov. is proposed. The type strain is CTD02-10-2^T (=JCM 33842^T=MCCC 1A16619^T).

Green Technology Approach for Reinforcement of Calcium Chloride Cured Sodium Alginate Films by Isolated Bacteria from Palm Oil Mill Effluent (POME)

The suitability of bacteria application as fillers to reinforce calcium chloride cured sodium alginate film was investigated through the determination of the physical, morphological and mechanical properties of composite films. There were six species of bacteria isolated from palm oil mill effluent sample. The bacteria sample selected for filler reinforcement has a sub-micron diameter of 0.83 ± 0.13 µm. The growth curve of selected bacteria revealed that four days of broth culture produced the maximum bacteria mass. The composite films were produced with reinforcement of 0.1 g, 0.2 g, 0.3 g and 0.4 g of bacteria respectively. Overall, the increment of bacteria mass resulted in the production of yellowish composite films with improved morphological, physical and mechanical properties. The results revealed that the composite films reinforced with 0.3 g and 0.4 g of bacteria appeared to have less curling on the surface of the film. The water absorption properties of the films were initially 140.74% and remained constant at an approximate of 200% after the reinforcement. The tensile strength properties showed a total increment of approximately 22.70% (from 36.10 ± 1.94 MPa to 44.29 ± 0.60 MPa). Based on the results, bacteria fillers were not able to enhance the elongation properties because only about 0.6% of overall increment was observed which was considered insignificant. It was concluded that the bacteria biomass has the potential to be used as fillers to reinforce calcium chloride cured sodium alginate film.

Micromonospora fluminis sp. nov., isolated from mountain river sediment

During a bioprospection of bacteria with antimicrobial activity, the actinomycete strain A38^T was isolated from a sediment sample of the Carpintero river located in the Gran Piedra Mountains, Santiago de Cuba province (Cuba). This strain was identified as a member of the genus Micromonospora by means of a polyphasic taxonomy study. Strain A38^T was an aerobic Gram-positive filamentous bacterium that produced single spores in a well-developed vegetative mycelium. An aerial mycelium was absent. The cell wall contained meso-diaminopimelic acid and the whole-cell sugars were glucose, mannose, ribose and xylose. The major cellular fatty acids were isoC_15:0, 10 methyl C_17:0, anteiso-C_17:0 and iso-C_17:0. The predominant menaquinones were MK-10(H₄) and MK-10(H6). Phylogenetic analysis of 16S rRNA gene sequences revealed that this strain was closely related to Micromonospora tulbaghiae DSM 45142^T (99.5 %), Micromonospora citrea DSM 43903^T (99.4 %), Micromonospora marina DSM 45555^T (99.4 %), Micromonospora maritima DSM 45782^T (99.3 %), Micromonospora sediminicola DSM 45794^T (99.3 %), Micromonospora aurantiaca DSM 43813^T (99.2 %) and Micromonospora chaiyaphumensis DSM 45246^T (99.2 %). The results of OrthoANIu analysis showed the highest similarity to Micromonospora chalcea DSM 43026^T (96.4 %). However, the 16S rRNA and gyrB gene sequence-based phylogeny and phenotypic characteristics provided support to distinguish strain A38^T as a novel species. On the basis of the results presented here, we propose to classify strain A38^T (=LMG 30467^T=CECT 30034^T) as the type strain of the novel species Micromonospora fluminis sp. nov.

Revisiting peptidoglycan sensing: interactions with host immunity and beyond

The interaction between host immunity and bacterial cells plays a pivotal role in a variety of human diseases. The bacterial cell wall component peptidoglycan (PG) is known to stimulate an immune response, which makes PG a distinctive recognition element for unveiling these complicated molecular interactions. Pattern recognition receptor (PRR) proteins are among the critical components of this system that initially recognize molecular patterns associated with microorganisms such as bacteria and fungi. These molecular patterns are mostly embedded in the bacterial or fungal cell wall structure and can be released and presented to the immune system in various situations. Nonetheless, detailed knowledge of this recognition is limited due to the diversity among the PG polymer and its fragments; the subsequent responses by multiple hosts add more complexity. Here, we discuss how our understanding of the role and molecular mechanisms of the well-studied PRR, the NOD-like receptors (NLRs), in the human immune system has evolved in recent years. We highlight the instances of other classes of proteins with similar behavior in the recognition of PG that have been identified in other microorganisms such as yeasts. These proteins are particularly interesting because a network of cellular interactions exists between human host cells, bacteria and yeast as a part of the normal human flora. To support our understanding of these interactions, we provide insight into the chemist's toolbox of peptidoglycan probes that aid in the investigations of the behaviors of these proteins and other biological contexts relevant to the sensing and recognition of peptidoglycan. The importance of these interactions in human health for the development of biomarkers and biotherapy is highlighted.

Lysis of cells of diverse bacteria by l,d-peptidases of Escherichia coli bacteriophages RB43, RB49 and T5

AIMS

The objective of this work was to study the antibacterial specificity and antibacterial effect of endolysins isolated from colibacteriophages RB43, RB49 and T5-as manifested on the exponential and stationary cell cultures of diverse bacteria depending on the growth stage, structure of peptidoglycan (PG) and antibiotic resistance.

METHODS AND RESULTS

Enzyme activity was assayed by the spectrophotometric method. Antimicrobial activity was estimated by the number of colony forming units (CFUs), with the results represented as logarithmic units. Morphological examination of bacterial cells was conducted using phase-contrast and scanning electron microscopy. The enzymes EndoT5, endolysin of bacteriophage T5, EndoRB43, endolysin of bacteriophage RB43 and EndoRB49, endolysin of bacteriophage RB49 turned out to be much less bacteriospecific than the corresponding Escherichia coli phages; they lysed bacteria of the genera Bacillus, Cellulomonas and Sporosarcina, whose PGs had different structures (A1γ, A4α and A4β) and chemical modifications (amidation). The specific lytic activity of phage enzymes was independent of the antibiotic resistance of bacterial cells and was higher when the cells were in the exponential, rather than stationary, growth phase. The analysis of morphological changes showed that the intermediate stage of the endolysin-induced lysis of bacterial cells was the formation of spheroplasts and protoplasts.

CONCLUSIONS

Endolysins of colibacteriophages RB49, RB43 and T5 have a wide spectrum of antibacterial action, which includes a number of diverse micro-organisms with different PG structures.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is a study of the bacterial selectivity of enzymes degrading bacterial cell wall in relation to the chemical structure of PG. It is shown that endolysins of bacteriophages RB49 and RB43 efficiently lyse cell wall of Gram-positive bacteria of the genus Bacillus and Gram-negative bacteria of the genus Pseudomonas (including an antibiotic-resistant strain). The number of bacterial cells is reduced by 3-6 orders of magnitude, which indicates good prospects for using these enzymes in biotechnology.

Vallicoccus soli gen. nov., sp. nov., a novel actinobacterium isolated from soil, and description of Vallicoccaceae fam. nov., Motilibacterales ord. nov

A novel Gram-stain-positive, aerobic, cocci-shaped actinobacterium, designated YIM 75000^T, was isolated from a soil sample collected from a dry-hot river valley in Yunnan Province, P.R. China. Growth was observed at 10-45 °C (optimal 37 °C), 0-8% (w/v) NaCl (optimal at 0-3% NaCl) and pH 6.0-8.0 (optimal at pH 7.3). The peptidoglycan contained LL-diaminopimelic acid, glycine, glutamic acid as well as alanine and its type was A3γ with an LL-Dpm-Gly interpeptide bridge. The major cellular fatty acids (> 10%) were C_16:0, Summed In Feature 3 (C_16:1 ω6c/C_16:1 ω7c) and C_17:1 ω8c. The predominant menaquinone was MK-9(H₄). The major whole-cell sugars contained rhamnose, ribose, arabinose and mannose. The DNA G+C content was 77.0 mol%. The 16S rRNA gene sequence similarities of strain YIM 75000^T with other species were less than 94%. Phylogenetic analyses based on 16S rRNA gene sequences and genome data, revealed that strain YIM 75000^T together with the genus Motilibacter formed a distinct phylogenetic lineage within the phylum Actinobacteria, separating them from members of all orders. Strain YIM 75000^T showed 73.4-73.7% average nucleotide identity and 19.5-19.7% digital DNA-DNA hybridization identity with the closely related genus Motilibacter. Based on the phenotypic, phylogenetic and chemotaxonomic data, it is proposed that the new isolate represents the nomenclature type of the novel species Vallicoccus soli gen. nov., sp. nov. (YIM 75000^T = DSM 45377^T = KCTC 49228^T = CGMCC 1.13844^T) which is the nomenclature type of the novel genus Vallicoccus gen. nov. within Vallicoccaceae fam. nov and Motilibacterales ord. nov in the phylum Actinobacteria. The family Vallicoccaceae fam. nov. and the order Motilibacterales (contains Vallicoccaceae fam. nov. and Motilibacteraceae Lee 2013) ord. nov. are formally proposed.

Lactococcus carnosus sp. nov. and Lactococcus paracarnosus sp. nov., two novel species isolated from modified-atmosphere packaged beef steaks

As part of a study investigating the spoilage microbiome of modified-atmosphere packaged beef from Germany, four novel strains of lactic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they could not be assigned to known species. The isolates were Gram-staining-positive, coccoid, facultatively anaerobic, non-motile, catalase-negative and oxidase-negative. Morphological, physiological and phylogenetic analysis revealed a distinct lineage within the genus Lactococcus , with Lactococcus piscium and Lactococcus plantarum as closest relatives. Results indicated that they represented two different novel species with two strains, (TMW 2.1612T/TMW 2.1613 and TMW 2.1615T/TMW 2.1614), respectively. The two strains of both novel species shared identical 16S rRNA gene sequences but a MLSA allowed their intraspecies differentiation. The 16S rRNA gene sequences of TMW 2.1612T and TMW 2.1615T had a similarity of 99.85 % to each other and a similarity of 99.85 and 99.78 % the most closely related type strain of Lactococcus piscium , respectively. However, the ANIb value between the respective type strains TMW 2.1612T and TMW 2.1615T, and the type strain of Lactococcus piscium was only 94.3 and 92.0 %, respectively, and 92.9 % between TMW 2.1612T and TMW 2.1615T. The in silico DDH estimate value between the respective type strain TMW 2.1612T and TMW 2.1615T and the most closely related type strain of Lactococcus piscium was only 59.9 and 48.9 %, respectively, and 51.1 % between TMW 2.1612T and TMW 2.1615T. Peptidoglycan type of strain TMW 2.1612T is Lys–Thr–Ala and major fatty acids are summed feature 8 and C16 : 0. Peptidoglycan type of strain TMW 2.1615T is Lys–Ala and major fatty acids are C16 : 0, C19 : 0cyclo ω8c and summed feature 8. On the basis of polyphasic evidence, the meat isolates represent two novel species of the genus Lactococcus , for which the names Lactococcus carnosus sp. nov and Lactococcus paracarnosus sp. nov are proposed. The designated respective type strains are TMW 2.1612T (=DSM 111016T =CECT 30115T) and TWM 2.1615T (=DSM 111017T =CECT 30116T).

Two Distinct Modes of Lysis Regulation in Campylobacter Fletchervirus and Firehammervirus Phages

Campylobacter phages are divided into two genera; Fletchervirus and Firehammervirus, showing only limited intergenus homology. Here, we aim to identify the lytic genes of both genera using two representative phages (F352 and F379) from our collection. We performed a detailed in silico analysis searching for conserved protein domains and found that the predicted lytic genes are not organized into lysis cassettes but are conserved within each genus. To verify the function of selected lytic genes, the proteins were expressed in E. coli, followed by lytic assays. Our results show that Fletchervirus phages encode a typical signal peptide (SP) endolysin dependent on the Sec-pathway for translocation and a holin for activation. In contrast, Firehammervirus phages encode a novel endolysin that does not belong to currently described endolysin groups. This endolysin also uses the Sec-pathway for translocation but induces lysis of E. coli after overexpression. Interestingly, co-expression of this endolysin with an overlapping gene delayed and limited cell lysis, suggesting that this gene functions as a lysis inhibitor. These results indicate that Firehammervirus phages regulate lysis timing by a yet undescribed mechanism. In conclusion, we found that the two Campylobacter phage genera control lysis by two distinct mechanisms.

β-Lytic Protease of Lysobacter capsici VKM B-2533T

Bacteriolytic enzymes are promising antimicrobial agents for developing new-generation drugs. Recently, we have isolated a β-lytic protease (BlpLc) from the culture liquid of Lysobacter capsici VKM B-2533^T. This BlpLc possesses a valuable property, not described for β-lytic proteases (Blps) earlier, of hydrolyzing living cells of Staphylococcus aureus 55 MRSA clinical isolate. This work phylogenetically characterized the BlpLc and investigated its properties. Analysis revealed a variability of pre-/pro-parts of Blp precursors. The mature BlpLc is the closest to the earlier annotated but not isolated Blp from Lysobacter sp. Root690. The biochemical characterization found conditions for the BlpLc general bacteriolytic activity relative to autoclaved S. aureus 209P cells to differ from that of earlier isolated Blp. Unexpected was the effect of serine (phenylmethylsulfonyl fluoride (PMSF)) and cysteine (p-chloromercuribenzoate (p-CMB)) protease inhibitors on BlpLc bacteriolytic and proteolytic activities. The specificity of BlpLc proteolytic action relative to hemoglobin, elastin, gelatin, collagen, azofibrin, myoglobin, ovalbumin, and ovamucoid was found. New types of peptide bonds—Gly-X, Ser-X, Lys-X, Ala-X, Val-X, Glu-X, and Phe-X—hydrolyzed by the enzyme in protein substrates were first revealed using MALDI-TOF. Turbidimetrically, the BlpLc was found to lyze living cells of S. aureus 209P, Micrococcus luteus B1819, and M. roseus B1236, which is important for expanding the enzyme’s applied properties.

Synthesis of Bacterial-Derived Peptidoglycan Cross-Linked Fragments

Peptidoglycan (PG) is the core structural motif of the bacterial cell wall. Fragments released from the PG serve as fundamental recognition elements for the immune system. The structure of the PG, however, encompasses a variety of chemical modifications among different bacterial species. Here, the applicability of organic synthetic methods to address this chemical diversity is explored, and the synthesis of cross-linked PG fragments, carrying biologically relevant amino acid modifications and peptide cross-linkages, is presented using solution and solid phase approaches.

Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum

Koalas (Phascolarctos cinereus) are highly specialized herbivorous marsupials that feed almost exclusively on Eucalyptus leaves, which are known to contain varying concentrations of many different toxic chemical compounds. The literature suggests that Lonepinella koalarum, a bacterium in the Pasteurellaceae family, can break down some of these toxic chemical compounds. Furthermore, in a previous study, we identified L. koalarum as the most predictive taxon of koala survival during antibiotic treatment. Therefore, we believe that this bacterium may be important for koala health. Here, we isolated a strain of L. koalarum from a healthy koala female and sequenced its genome using a combination of short-read and long-read sequencing. We placed the genome assembly into a phylogenetic tree based on 120 genome markers using the Genome Taxonomy Database (GTDB), which currently does not include any L. koalarum assemblies. Our genome assembly fell in the middle of a group of Haemophilus, Pasteurella and Basfia species. According to average nucleotide identity and a 16S rRNA gene tree, the closest relative of our isolate is L. koalarum strain Y17189. Then, we annotated the gene sequences and compared them to 55 closely related, publicly available genomes. Several genes that are known to be involved in carbohydrate metabolism could exclusively be found in L. koalarum relative to the other taxa in the pangenome, including glycoside hydrolase families GH2, GH31, GH32, GH43 and GH77. Among the predicted genes of L. koalarum were 79 candidates putatively involved in the degradation of plant secondary metabolites. Additionally, several genes coding for amino acid variants were found that had been shown to confer antibiotic resistance in other bacterial species against pulvomycin, beta-lactam antibiotics and the antibiotic efflux pump KpnH. In summary, this genetic characterization allows us to build hypotheses to explore the potentially beneficial role that L. koalarum might play in the koala intestinal microbiome. Characterizing and understanding beneficial symbionts at the whole genome level is important for the development of anti- and probiotic treatments for koalas, a highly threatened species due to habitat loss, wildfires, and high prevalence of Chlamydia infections.

Motilibacter deserti sp. nov. and Motilibacter aurantiacus sp. nov., two novel actinobacteria isolated from soil of Cholistan Desert and emended description of the genus Motilibacter

Two novel actinobacterial strains, designated as E257^T and K478^T, were isolated from hyper-arid soil samples collected in Cholistan Desert, Pakistan. Comparative analysis of 16S rRNA genes showed that strains E257^T and K478^T were assigned to the genus Motilibacter, being their closest relative M. rhizosphaerae RS-16^T with 97.3% and 96.7% similarities, respectively. The sequence similarity between strain E257^T and K478^T was 98.9%. Phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic analysis based on multiple genes of conserved core proteins exhibited that these two strains belonged to the genus Motilibacter and formed a robust cluster separated from the two type species of the genus Motilibacter. Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), digital DNA-DNA hybridization (dDDH) values and Percentage of Conserved Proteins (POCP) calculated from the complete genome sequences indicated strains E257^T and K478^T were assigned into genus Motilibacter but clearly separated from each other and from the other species of the genus Motilibacter with values below the thresholds for species delineation. The two isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Motilibacter and also confirmed the differentiation from their closest species. The obtained results demonstrated that strains E257^T and K478^T represent two novel species of the genus Motilibacter, for which the names Motilibacter desertisp. nov. (type strain E257^T = JCM 33651^T = CGMCC 1.17159^T) and Motilibacter aurantiacus sp. nov. (type strain K478^T =JCM 33652^T =CGMCC 1.17229^T) are proposed.

Synergies with and Resistance to Membrane-Active Peptides

Membrane-active peptides (MAPs) have long been thought of as the key to defeating antimicrobial-resistant microorganisms. Such peptides, however, may not be sufficient alone. In this review, we seek to highlight some of the common pathways for resistance, as well as some avenues for potential synergy. This discussion takes place considering resistance, and/or synergy in the extracellular space, at the membrane, and during interaction, and/or removal. Overall, this review shows that researchers require improved definitions of resistance and a more thorough understanding of MAP-resistance mechanisms. The solution to combating resistance may ultimately come from an understanding of how to harness the power of synergistic drug combinations.

Rubrobacter tropicus sp. nov. and Rubrobacter marinus sp. nov., isolated from deep-sea sediment of the South China Sea

Two novel Gram-stain-positive bacteria, designated as SCSIO 52909^T and SCSIO 52915^T, were isolated from a deep-sea sediment sample collected at about 3448 m water depth of the South China Sea. Phenotypic, chemotaxonomic and genomic characteristics were investigated. These strains were aerobic and tested positive for catalase activity, oxidase activity and nitrate reduction. Optimal growth occurred at 28 °C, pH 7 and 3% salinity over 14 days cultivation. Its peptidoglycan structure was type A3α (l-Lys-l-Ala) and the only menaquinone was MK-8. Both strains possessed diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid, an unidentified glycolipid and an unidentified phospholipid. Their major fatty acids differed, but both contained iso-branched components of C_16 : 0 12-methyl. Genome sequencing revealed two large genomes of 4.58 Mbp with G+C content of 67.0 mol% in SCSIO 52909^T and of 4.42 Mbp with G+C content of 69.1 % in SCSIO 52915^T. The two novel strains encoded genes for metabolism that are absent in most other Rubrobacter species, and possessed many more gene copy numbers of alkaline phosphatase and thioredoxin reductase. Results of gANI and 16S rRNA gene analyses suggested that the two strains represent two new species, with 74.9, 95.0 % pairwise similarity between each other, and less than 74.3 and 93.5 % to other recognized Rubrobacter species, respectively. In the phylogenetic analysis, strains SCSIO 52909^T and SCSIO 52915^T were separately clustered together and formed a well-separated phylogenetic branch distinct from the other known species in the genus Rubrobacter. Based on the data presented here, these two strains should be recognized as two new species in the genus Rubrobacter, for which the names Rubrobacter tropicus sp. nov., with the type strain SCSIO 52909^T (=KCTC 49412^T=CGMCC 1.13853^T), and Rubrobacter marinus sp. nov., with the type strain SCSIO 52915^T (=KCTC 49411^T=CGMCC 1.13852^T), are proposed.

Brevibacillus migulae sp. nov., isolated from a Yellow River sediment sample

Strain CFH S0501^T, a novel Gram-stain-positive, aerobic, rod-shaped, endospore-forming and motile micro-organism with peritrichous flagella, was isolated from a sediment sample collected from the Yellow River in Henan Province, PR China. Optimum growth was observed at 28 °C, pH 7.0 and without NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain belonged to the genus Brevibacillus and was closely related to Brevibacillus centrosporus DSM 8445^T and Brevibacillus ginsengisoli Gsoil 3088^T (with 96.8 and 96.7 % sequence similarity, respectively). The predominant menaquinone was MK-7. Major cellular fatty acids were anteiso-C_15 : 0 and iso-C_15 : 0. Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unidentified phospholipids and an unidentified polar lipid. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid. The genome size was 5.26 Mbp with a G+C content of 49.7 mol%. The average nucleotide identity (ANI) and in silico DNA-DNAhybridization (DDH) values between CFH S0501^T and the other species of the genus Brevibacillus were found to be low (ANIm <86.11 %, ANIb <70.30 % and DDH <25.00 %). Based on physiological properties, chemotaxonomic characteristics and low ANI and DDH results, strain CFH S0501^T is considered to represent a novel species, for which the name Brevibacillus migulae sp. nov. is proposed. The type strain is CFH S0501^T (=DSM 29940^T=BCRC 80809^T).

Staphylococcus ursi sp. nov., a new member of the 'Staphylococcus intermedius group' isolated from healthy black bears

Six Staphylococcus strains were isolated from healthy black bears (Ursus americanus) in the Great Smoky Mountains National Park, Tennessee, USA. Phylogenetic analysis based on complete genome, 16S rRNA, dnaJ, hsp60, rpoB and sodA genes, and MALDI-TOF-MS main spectral profiles revealed that the strains belonged to one species and showed the closest relatedness to members of the 'Staphylococcus intermedius group' (SIG), which include Staphylococcus intermedius, Staphylococcus pseudintermedius, Staphylococcus delphini and Staphyloccoccus cornubiensis. The strains were positive in SIG-specific and negative in individual species-specific PCR assays for the nuc gene. The strains can be differentiated from the other SIG species by the absence of sucrose fermentation, from S. intermedius DSM 20373^T, S. pseudintermedius CCUG 49543^T and S. cornubiensis DSM 105366^T by the absence of methyl β-d-glucopyranoside fermentation and from S. delphini DSM 20771^T by fermentation of trehalose. DNA relatedness of the type strain MI 10-1553^T with the type strains of S. delphini, S. pseudintermedius, S. intermedius and S. cornubiensis was ≤48.2 % by digital DNA-DNA hybridization and ≤92.3 % by average nucleotide identity calculations. Iso-_C15:0, anteiso-C_15 : 0 and anteiso-C_17 : 0 were the most common fatty acids. Polar lipids consisted of phosphadidylglycerols, phospholipids, glycolipid, diphosphatidylglycerol and aminophospholipid. Cell-wall peptidoglycan was of type A3α l-Lys-Gly₃ (Ser; similar to A11.2 and A11.3). The respiratory quinone belonged to menaquinone 7 (MK-7). The G+C content of MI 10-1553^T was 39.3 mol%. The isolated strains represent a novel species of the genus Staphylococcus, for which we propose the name Staphylococcus ursi sp. nov. The type strain is MI 10-1553^T (=ATCC TSD-55^T=CCOS 1900^T).

Gulosibacter macacae sp. nov., a novel actinobacterium isolated from Macaca mulatta faeces

A novel Gram-stain-positive, aerobic, non-spore-forming, irregular short rod-shaped actinobacterial strain, designated YIM 102482-1T, was isolated from the faeces of Macaca mulatta. Strain YIM 102482-1T grew optimally at 30–37 °C, at pH 8.0 and in the presence of 1.0–3.0% (w/v) NaCl. Similarly, analysis based on 16S rRNA gene sequences showed that strain YIM 102482-1T was a member of the genus Gulosibacter and most closely related to Gulosibacter feacalis NBRC 15706T (97.6 %), Gulosibacter bifidus NBRC 103089T (97.6 %), Gulosibacter chungangensis KCTC 13959T (96.4 %) and Gulosibacter molinativorax DSM 13485T (96.0 %), respectively. Furthermore, phylogenetic trees based on 16S rRNA gene sequences and genomic sequences demonstrated that strain YIM 102482-1T formed a distinct branch with all type strains of the genus Gulosibacter . The major whole-cell sugars and cellular fatty acids (>10.0 %) were ribose and rhamnose, and anteiso-C15 : 0, iso-C16 : 0 and C16 : 0, respectively. The predominant menaquinone was MK-9, and 2,4-diaminobutyric acid and ornithine were the diagnostic diamino acids in the cell-wall peptidoglycan. The dominant polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipid. The DNA G+C content of YIM 102482-1T was 63.0 mol%. Based on analysis results of physiological, biochemical and chemotaxonomic data, strain YIM 102482-1T represents a novel species of the genus Gulosibacter , for which the name Gulosibacter macacae sp. nov. is proposed. The type strain is YIM 102482-1T(=DSM 102156T=CCTCC AB 2016023T).

Anthrax toxin component, Protective Antigen, protects insects from bacterial infections

Anthrax is a major zoonotic disease of wildlife, and in places like West Africa, it can be caused by Bacillus anthracis in arid nonsylvatic savannahs, and by B. cereus biovar anthracis (Bcbva) in sylvatic rainforests. Bcbva-caused anthrax has been implicated in as much as 38% of mortality in rainforest ecosystems, where insects can enhance the transmission of anthrax-causing bacteria. While anthrax is well-characterized in mammals, its transmission by insects points to an unidentified anthrax-resistance mechanism in its vectors. In mammals, a secreted anthrax toxin component, 83 kDa Protective Antigen (PA83), binds to cell-surface receptors and is cleaved by furin into an evolutionary-conserved PA20 and a pore-forming PA63 subunits. We show that PA20 increases the resistance of Drosophila flies and Culex mosquitoes to bacterial challenges, without directly affecting the bacterial growth. We further show that the PA83 loop known to be cleaved by furin to release PA20 from PA63 is, in part, responsible for the PA20-mediated protection. We found that PA20 binds directly to the Toll activating peptidoglycan-recognition protein-SA (PGRP-SA) and that the Toll/NF-κB pathway is necessary for the PA20-mediated protection of infected flies. This effect of PA20 on innate immunity may also exist in mammals: we show that PA20 binds to human PGRP-SA ortholog. Moreover, the constitutive activity of Imd/NF-κB pathway in MAPKK Dsor1 mutant flies is sufficient to confer the protection from bacterial infections in a manner that is independent of PA20 treatment. Lastly, Clostridium septicum alpha toxin protects flies from anthrax-causing bacteria, showing that other pathogens may help insects resist anthrax. The mechanism of anthrax resistance in insects has direct implications on insect-mediated anthrax transmission for wildlife management, and with potential for applications, such as reducing the sensitivity of pollinating insects to bacterial pathogens.

Arthrobacter yangruifuii sp. nov. and Arthrobacter zhaoguopingii sp. nov., two new members of the genus Arthrobacter

Four unknown strains belonging to the genus Arthrobacter were isolated from plateau wildlife on the Qinghai-Tibet Plateau of PR China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four isolates were separated into two clusters. Cluster I (strains 785^T and 208) had the greatest 16S rRNA gene sequence similarity to Arthrobacter citreus (98.6 and 98.7 %, respectively), Arthrobacter luteolus (98.0 and 98.1%, respectively), Arthrobacter gandavensis (97.9 and 98.0 %, respectively) and Arthrobacter koreensis (97.6 and 97.7 %, respectively). Likewise, cluster II (strains J391^T and J915) had the highest sequence similarity to Arthrobacter ruber (98.6 and 98.3 %, respectively) and Arthrobacter agilis (98.1 and 97.9  %, respectively). Average nucleotide identity and the digital DNA-DNA hybridization values illustrated that the two type strains, 785^T and J391^T, represented two separate novel species that are distinct from all currently recognized species in the genus Arthrobacter. These strains had DNA G+C contents of 66.0-66.1 mol% (cluster I) and 68.0 mol% (cluster II). The chemotaxonomic properties of strains 785^T and J391^T were in line with those of the genus Arthrobacter: anteiso-C_15:0 (79.3 and 40.8 %, respectively) as the major cellular fatty acid, MK-8(H₂) (65.8 %) or MK-9(H₂) (75.6 %) as the predominant respiratory quinone, a polar lipid profile comprising diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipids and phospholipid, and A3α or A4α as the cell wall peptidoglycan type. On the basis of our results, two novel species in the genus Arthrobacter are proposed, namely Arthrobacter yangruifuii sp. nov. (type strain, 785^T=CGMCC 1.16725^T=GDMCC 1.1592^T=JCM 33491^T) and Arthrobacter zhaoguopingii sp. nov. (type strain, J391^T=CGMCC 1.17382^T=GDMCC 1.1667^T=JCM 33841^T).

d-Amino acids in antimicrobial peptides: a potential approach to treat and combat antimicrobial resistance

Antimicrobial resistance is one of the leading challenges in the human healthcare segment. Advances in antimicrobial resistance have triggered exploration of natural alternatives to stabilize its seriousness. Antimicrobial peptides are small, positively charged oligopeptides that are as potent as commercially available antibiotics against a wide spectrum of organisms, such as Gram-positive bacteria, Gram-negative bacteria, viruses, and fungal strains. In addition to their antibiotic capabilities, these peptides possess anticancer activity, activate the immune response, and regulate inflammation. Peptides have distinct modes of action and fall into various categories due to their amino acid composition. Although antimicrobial peptides specifically target the bacterial cytoplasmic membrane, they can also target the cell nucleus and protein synthesis. Owing to the increasing demand for novel treatments against the threat of antimicrobial resistance, naturally synthesized peptides are a beneficial development concept. Antimicrobial peptides are pervasive and can easily be modified using de-novo synthesis technology. Antimicrobial peptides can be isolated from natural resources such as humans, plants, bacteria, and fungi. This review gives a brief overview of antimicrobial peptides and their diastereomeric composition. Other current trends, the future scope of antimicrobial peptides, and the role of d-amino acids are also discussed, with a specific emphasis on the design and development of new drugs.

Fundicoccus ignavus gen. nov., sp. nov., a novel genus of the family Aerococcaceae isolated from bulk tank milk

Three strains of a Gram-stain-positive, catalase-negative, facultative anaerobic, and coccoid species were isolated from German bulk tank milk. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that the three strains (WS4937^T, WS4759 and WS5303) constitute an independent phylogenetic lineage within the family Aerococcaceae with Facklamia hominis CCUG 36813^T (93.7-94.1 %) and Eremococcus coleocola M1831/95/2^T (93.5 %) as most closely related type species. The unclassified strains demonstrated variable growth with 6.5 % (w/v) NaCl and tolerated pH 6.5-9.5. Growth was observed from 12 to 39 °C. Their cell-wall peptidoglycan belongs to the A1α type (l-Lys-direct) consisting of alanine, glutamic acid and lysine. The predominant fatty acids were C_16 : 1 ω9c, C_16 : 0 and C_18 : 1 ω9c and in the polar lipids profile three glycolipids, a phospholipid, phosphatidylglycerol, phosphoglycolipid and diphosphatidylglycerol were found. The G+C content of strain WS4937^T was 37.4 mol% with a genome size of ~3.0 Mb. Based on phylogenetic, phylogenomic and biochemical characterizations, the isolates can be demarcated from all other genera of the family Aerococcaceae and, therefore, the novel genus Fundicoccus gen. nov. is proposed. The type species of the novel genus is Fundicoccus ignavus gen. nov., sp. nov. WS4937^T (=DSM 109652^T=LMG 31441^T).

The Role of the Bacterial Muramyl Dipeptide in the Regulation of GLP-1 and Glycemia

The host's intestinal microbiota contributes to endocrine and metabolic responses, but a dysbiosis in this environment can lead to obesity and insulin resistance. Recent work has demonstrated a role for microbial metabolites in the regulation of gut hormones, including the metabolic hormone, glucagon-like peptide-1 (GLP-1). Muramyl dipeptide (MDP) is a bacterial cell wall component which has been shown to improve insulin sensitivity and glucose tolerance in diet-induced obese mice by acting through the nucleotide oligomerization domain 2 (NOD2) receptor. The purpose of this study was to understand the effects of MDP on GLP-1 secretion and glucose regulation. We hypothesized that MDP enhances glucose tolerance by inducing intestinal GLP-1 secretion through NOD2 activation. First, we observed a significant increase in GLP-1 secretion when murine and human L-cells were treated with a fatty acid MDP derivative (L18-MDP). Importantly, we demonstrated the expression of the NOD2 receptor in mouse intestine and in L-cells. In mice, two intraperitoneal injections of MDP (5 mg/kg body weight) caused a significant increase in fasting total GLP-1 in chow-fed mice, however this did not lead to an improvement in oral glucose tolerance. When mice were exposed to a high-fat diet, they eventually lost this MDP-induced GLP-1 release. Finally, we demonstrated in L-cells that hyperglycemic conditions reduce the mRNA expression of NOD2 and GLP-1. Together these findings suggest MDP may play a role in enhancing GLP-1 during normal glycemic conditions but loses its ability to do so in hyperglycemia.

Exploiting phage receptor binding proteins to enable endolysins to kill Gram-negative bacteria

Bacteriophage-encoded endolysins degrading the bacterial peptidoglycan are promising antibacterials for combating antibiotic-resistant bacteria. However, endolysins have limited use against Gram-negative bacteria, since the outer membrane prevents access to the peptidoglycan. Here, we present Innolysins, an innovative concept for engineering endolysins to exert antibacterial activity against Gram-negative bacteria. Innolysins combine the enzymatic activity of endolysins with the binding capacity of phage receptor binding proteins (RBPs). As proof-of-concept, we constructed 12 Innolysins by fusing phage T5 endolysin and RBP Pb5 in different configurations. One of these, Innolysin Ec6 displayed antibacterial activity against Escherichia coli only in the presence of Pb5 receptor FhuA, leading to 1.22 ± 0.12 log reduction in cell counts. Accordingly, other bacterial species carrying FhuA homologs such as Shigella sonnei and Pseudomonas aeruginosa were sensitive to Innolysin Ec6. To enhance the antibacterial activity, we further constructed 228 novel Innolysins by fusing 23 endolysins with Pb5. High-throughput screening allowed to select Innolysin Ec21 as the best antibacterial candidate, leading to 2.20 ± 0.09 log reduction in E. coli counts. Interestingly, Innolysin Ec21 also displayed bactericidal activity against E. coli resistant to third-generation cephalosporins, reaching a 3.31 ± 0.53 log reduction in cell counts. Overall, the Innolysin approach expands previous endolysin-engineering strategies, allowing customization of endolysins by exploiting phage RBPs to specifically target Gram-negative bacteria.

Isoptericola halalbus sp. nov., a halotolerant actinobacterium isolated from saline lake sediment

A novel Gram-stain-positive bacterium, designated CFH 91151^T, was isolated from sediment collected from a saline lake in Yuncheng, Shanxi Province, PR China. Cells of strain CFH 91151^T were rod-or v-shaped, aerobic, non-motile, non-spore-forming and halotolerant. Results of 16S rRNA gene sequence analysis revealed that strain CFH 91151^T was closely related to Isoptericola variabilis MX5^T and Isoptericola nanjingensis H17^T (98.7 and 98.4% sequence similarity, respectively). The strain grew at 4-45 °C, pH 5.0-9.0 and with 0-14.0 % (w/v) NaCl. Cells were positive for catalase, nitrate was not used and H₂S was not produced. Major cellular fatty acids were anteiso-C_15 : 0 (62.76 %), anteiso-C_17 : 0 (12.09 %) and iso-C_15 : 0 (9.46 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids and three unidentified glycolipids. The menaquinone was MK-9 (H4). The genome size was 4.10 Mbp with a G+C content of 72.4 mol%. The average amino acid identity (ANI) and in silico DNA-DNA hybridization (DDH) values between CFH 91151^T and the other species of the genus Isoptericola were found to be low (ANIm <87.19 %, ANIb <84.38 % and DDH <29.30 %). Based on physiological properties, chemotaxonomic characteristics and low ANI and DDH results, strain CFH 91151^T is considered to represent a novel species, for which the name Isoptericola halalbus sp. nov. is proposed. The type strain is CFH 91151^T (=DSM 105976^T=KCTC 49061^T).

Gordonia crocea sp. nov. and Gordonia spumicola sp. nov. isolated from sludge of a wastewater treatment plant

Two novel actinobacteria, designated NBRC 107696^T and NBRC 107697^T, were isolated from sludge samples from a wastewater treatment plant and their taxonomic positions were investigated by a polyphasic approach. The cells of the strains were aerobic, rod-shaped, non-motile and non-endospore-forming. The strains contained glutamic acid, alanine and meso-diaminopimelic acid in the peptidoglycan. Galactose and arabinose were detected as cell-wall sugars. The predominant menaquinone was identified as MK-9(H₂) and the major fatty acids were C_{16  :  0}, C_18 : 1ω9c and C_16 : 1ω7c. The DNA G+C contents of NBRC 107696^T and NBRC 107697^T were 68.07 and 68.99 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequence comparisons revealed that NBRC 107696^T and NBRC 107697^T were a clade with members of the genus Gordonia. The highest 16S rRNA gene sequence similarity values were obtained with Gordonia araii IFM 10211^T (98.9 %) for NBRC 107697^T, and Gordonia malaquae IMMIB WWCC-22^T, Gordonia neofelifaecis AD-6^T and Gordonia humi CC-12301^T (98.1 %) for NBRC 107696^T, respectively. The digital DNA-DNA relatedness data coupled with the combination of genotypic and phenotypic data indicated that the two strains are representatives of two novel separate species. The names proposed to accommodate these two strains are Gordonia spumicola sp. nov. and Gordonia crocea sp. nov., and the type strains are NBRC 107696^T (=IFM 10067^T=TBRC 11239^T) and NBRC 107697^T (=IFM 10881^T=TBRC 11240^T), respectively.

Auraticoccus cholistanensis sp. nov., an actinomycete isolated from soil of the Cholistan Desert, and emended description of the genus Auraticoccus

A Gram-stain-positive, aerobic, non-motile and non-spore-forming actinobacterium, designated as F435^T, was isolated from soil sample collected from the Cholistan Desert, Pakistan. The taxonomic position of the strain was established by using a polyphasic taxonomic approach. The cells were coccoid-shaped and found in single or arrangement of pairs. The novel strain grew at 15‒37 °C (optimum, 25‒30 °C), pH 7‒11 (optimum, pH 7-8) and in the presence of 0‒8% (w/v) NaCl (optimum, 0 %). Results of blast analysis based on 16S rRNA gene sequences showed that Auraticoccus monumenti MON 2.2^T was its closest relative with 97.4 % similarity followed by Desertihabitans aurantiacus CPCC 204711^T (95.2 %). In phylogenetic trees, strain F435^T formed a robust cluster with the only member of the genus Auraticoccus. The peptidoglycan isomer present in the cell wall was ll-diaminopimelic acid. The major fatty acid was determined to be anteiso-C_15 : 0. Characteristic polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol, phosphoglycolipids and glycolipids. The predominant menaquinone was MK-9(H₄). The genomic G+C content was calculated as 73.5 mol%. The digital DNA-DNA hybridization (GGDC) and average nucleotide identity (ANI) values between strain F435^T and A. monumenti MON 2.2^T were 24.6 and 81.8 %, respectively. Based on the results of phenotypic, chemotaxonomic, phylogenetic and phylogenomic analyses, strain F435^T represents a novel specie of the genus Auraticoccus, for which the name Auraticoccus cholistanensis sp. nov. is proposed. The type strain is F435^T (=JCM 33648^T=CGMCC 1.17443^T). The description of the genus Auraticoccus has also been emended.

The bacterial community and metabolome dynamics and their interactions modulate fermentation process of whole crop corn silage prepared with or without inoculants

Multi‐omics approach was adopted to investigate the modulation of bacterial microbiota and metabolome as well as their interactions in whole crop corn ensiling systems by inoculating homofermentative Lactobacillus plantarum or heterofermentative Lactobacillus buchneri. Inoculations of the two different inoculants resulted in substantial differences in microbial community and metabolic composition as well as their dynamics in ensiled corn. Inoculants also altered the correlations of microbiota in different manners, and various keystone species were identified in corn silages with different treatments. Many metabolites with biofunctional activities like bacteriostatic, antioxidant, central nervous system inhibitory and anti‐inflammatory were found in the present silage. A constitutive difference in microbiota dynamics was found for several pathways, which were upregulated by specific taxa in middle stage of fermentation, and widespread associations between metabolites with biofunctions and the species of lactic acid bacteria dominated in silage were observed. Multiple microbial and metabolic structures and dynamics were correlated and affected the fermentation process of the corn ensiling systems. Results of the current study improve our understanding of the complicated biological process underlying silage fermentation and provide a framework to re‐evaluate silages with biofunctions, which may contribute to target‐based regulation methods to produce functional silage for animal production.

Diverse Pathway to Obtain Antibacterial and Antifungal Agents Based on Silica Particles Functionalized by Amino and Phenyl Groups with Cu(II) Ion Complexes

Production of environmentally friendly multitasking materials is among the urgent challenges of chemistry and ecotechnology. The current research paper describes the synthesis of amino-/silica and amino-/phenyl-/silica particles using a one-pot sol-gel technique. CHNS analysis and titration demonstrated a high content of functional groups, while scanning electron microscopy revealed their spherical form and ∼200 nm in size. X-ray photoelectron spectroscopy data testified that hydrophobic groups reduced the number of water molecules and protonated amino groups on the surface, increasing the portion of free amino groups. The complexation with Cu(II) cations was used to analyze the sorption capacity and reactivity of the aminopropyl groups and to enhance the antimicrobial action of the samples. Antibacterial activities of suspensions of aminosilica particles and their derivative forms containing adsorbed copper(II) ions were assayed against Gram-positive (Staphylococcus aureus ATCC 25923) and Gram-negative bacteria (Escherichia coli ATCC 25922 and Pseudomonas aeruginosa ATCC 27853). Meanwhile, antifungal activity was tested against fungi (Candida albicans UCM Y-690). According to zeta potential measurements, its value could be depended on the suspension concentration, and it was demonstrated that the positively charged suspension had higher antibacterial efficiency. SiO₂/-C₆H₅/-NH₂ + Cu(II) sample's water suspension (1%) showed complete growth inhibition of the bacterial culture on the solid medium. The antimicrobial activity could be due to occurrence of multiple and nonspecific interactions between the particle surfaces and the surface layers of bacteria or fungi.

Two Glycosyl 1-Phosphate Polymers and Teichulosonic Acid from Glutamicibacter protophormiae VKM Ac-2104T Cell Wall

Two glycosyl 1-phosphate polymers containing monoglycosyl 1-phosphate, -6)-α-D-Glcp-(1-P-, and diglycosyl 1-phosphate, -6)-α-D-GalpNAc-(1→6)-α-D-GlcpNAc-(1-P-, in the repeating unit were identified in the cell wall of Glutamicibacter protophormiae VKM Ac-2104^T (formerly, Arthrobacter protophormiae). The structures of these polymers were described for the first time in prokaryotes. Teichulosonic acid, the third identified polymer, with 3-deoxy-D-glycero-α-D-galacto-non-2-ulopyranosonic acid (Kdn) and β-D-glucopyranose residues in the main chain, →6)-β-D-Glcp-(1→8)-α-Kdn-(2→, has been previously detected in a number of actinobacteria. The structures of these glycopolymers were established based on the results of chemical analysis and one-dimensional ¹H, ¹³C, and ³¹P NMR spectroscopy using two-dimensional homonuclear (¹H,¹H COZY, TOCSY, ROESY) and heteronuclear (¹H,¹³C HSQC, HSQC-TOCSY, HMBC, and ¹H,³¹P HMBC) techniques.