Proteomic Analysis Reveals a Biofilm-Like Behavior of Planktonic Aggregates of Staphylococcus epidermidis Grown Under Environmental Pressure/Stress

Cooperation of quorum sensing and central carbon metabolism in the pathogenesis of Gram-positive bacteria

Quorum sensing (QS), an integral component of bacterial communication, is essential in coordinating the collective response of diverse bacterial pathogens. Central carbon metabolism (CCM), serving as the primary metabolic hub for substances such as sugars, lipids, and amino acids, plays a crucial role in the life cycle of bacteria. Pathogenic bacteria often utilize CCM to regulate population metabolism and enhance the synthesis of specific cellular structures, thereby facilitating in adaptation to the host microecological environment and expediting infection. Research has demonstrated that QS can both directly or indirectly affect the CCM of numerous pathogenic bacteria, thus altering their virulence and pathogenicity. This article reviews the interplay between QS and CCM in Gram-positive pathogenic bacteria, details the molecular mechanisms by which QS modulates CCM, and lays the groundwork for investigating bacterial pathogenicity and developing innovative infection treatment drugs.

Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria

Sulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses complementary methodologies, viz., transcriptome-wide marker gene panel mapping and gene clustering analysis to decipher the stress mechanisms in four SRB. Here, the accessible RNA-sequencing data from the public domains were mined to identify the key transcriptional signatures. Crucial transcriptional candidate genes of Desulfovibrio spp. were accomplished and validated the gene cluster prediction. In addition, the unique transcriptional signatures of Oleidesulfovibrio alaskensis (OA-G20) at graphene and copper interfaces were discussed using in-house RNA-sequencing data. Furthermore, the comparative genomic analysis revealed 12,821 genes with translation, among which 10,178 genes were in homolog families and 2643 genes were in singleton families were observed among the 4 genomes studied. The current study paves a path for developing predictive deep learning tools for interpretable and mechanistic learning analysis of the SRB gene regulation.

The non-attached biofilm aggregate

Biofilms have conventionally been perceived as dense bacterial masses on surfaces, following the five-step model of development. Initial biofilm research focused on surface-attached formations, but detached aggregates have received increasing attention in the past decade due to their pivotal role in chronic infections. Understanding their nature sparked fervent discussions in biofilm conferences and scientific literature. This review consolidates current insights on non-attached aggregates, offering examples of their occurrence in nature and diseases. We discuss their formation and dispersion mechanisms, resilience to antibiotics and immune-responses, drawing parallels to surface-attached biofilms. Moreover, we outline available in vitro models for studying non-attached aggregates.

Skin-to-blood pH shift triggers metabolome and proteome global remodelling in Staphylococcus epidermidis

Staphylococcus epidermidis is one of the most common bacteria of the human skin microbiota. Despite its role as a commensal, S. epidermidis has emerged as an opportunistic pathogen, associated with 80% of medical devices related infections. Moreover, these bacteria are extremely difficult to treat due to their ability to form biofilms and accumulate resistance to almost all classes of antimicrobials. Thus new preventive and therapeutic strategies are urgently needed. However, the molecular mechanisms associated with S. epidermidis colonisation and disease are still poorly understood. A deeper understanding of the metabolic and cellular processes associated with response to environmental factors characteristic of SE ecological niches in health and disease might provide new clues on colonisation and disease processes. Here we studied the impact of pH conditions, mimicking the skin pH (5.5) and blood pH (7.4), in a S. epidermidis commensal strain by means of next-generation proteomics and 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes occurring during a sudden pH change, simulating the skin barrier break produced by a catheter. We found that exposure of S. epidermidis to skin pH induced oxidative phosphorylation and biosynthesis of peptidoglycan, lipoteichoic acids and betaine. In contrast, at blood pH, the bacterial assimilation of monosaccharides and its oxidation by glycolysis and fermentation was promoted. Additionally, several proteins related to virulence and immune evasion, namely extracellular proteases and membrane iron transporters were more abundant at blood pH. In the situation of an abrupt skin-to-blood pH shift we observed the decrease in the osmolyte betaine and changes in the levels of several metabolites and proteins involved in cellular redoxl homeostasis. Our results suggest that at the skin pH S. epidermidis cells are metabolically more active and adhesion is promoted, while at blood pH, metabolism is tuned down and cells have a more virulent profile. pH increase during commensal-to-pathogen conversion appears to be a critical environmental signal to the remodelling of the S. epidermidis metabolism toward a more pathogenic state. Targeting S. epidermidis proteins induced by pH 7.4 and promoting the acidification of the medical device surface or surrounding environment might be new strategies to treat and prevent S. epidermidis infections.

Host Environment Shapes S. aureus Social Behavior as Revealed by Microscopy Pattern Formation and Dynamic Aggregation Analysis

Understanding how bacteria adapt their social behavior to environmental changes is of crucial importance from both biological and clinical perspectives. Staphylococcus aureus is among the most common infecting agents in orthopedics, but its recalcitrance to the immune system and to antimicrobial treatments in the physiological microenvironment are still poorly understood. By means of optical and confocal microscopy, image pattern analysis, and mathematical modeling, we show that planktonic biofilm-like aggregates and sessile biofilm lifestyles are two co-existing and interacting phases of the same environmentally adaptive developmental process and that they exhibit substantial differences when S. aureus is grown in physiological fluids instead of common lab media. Physicochemical properties of the physiological microenvironment are proposed to be the key determinants of these differences. Besides providing a new tool for biofilm phenotypic analysis, our results suggest new insights into the social behavior of S. aureus in physiological conditions and highlight the inadequacy of commonly used lab media for both biological and clinical studies of bacterial development.

Comparative proteomics of Brucella melitensis is a useful toolbox for developing prophylactic interventions in a One-Health context

Brucellosis caused by Brucella melitensis is a zoonosis frequently reported in the Mediterranean and Middle-East regions and responsible for important economic losses and reduced animal welfare. To date, current strategies applied to control or eradicate the disease relies on diagnostic tests that suffer from limited specificity in non-vaccinated animals; while prophylactic measures, when applied, use a live attenuated bacterial strain characterized by residual virulence on adult pregnant animals and difficulties in distinguishing vaccinated from infected animals. To overcome these issues, studies are desired to elucidate the bacterial biology and the pathogenetic mechanisms of both the vaccinal strain and the pathogenic strains. Proteomics has a potential in tackling issues of One-Health concern; here, we employed label-free shotgun proteomics to investigate the protein repertoire of the vaccinal strain B. melitensis Rev.1 and compare it with the proteome of the Brucella melitensis 16 M, a reference strain representative of B. melitensis field strains. Comparative proteomics profiling underlines common and diverging traits between the two strains. Common features suggest the potential biochemical routes responsible for the residual virulence of the vaccinal strain, whilst the diverging traits are suggestive biochemical signatures to be further investigated to provide an optimized diagnostic capable of discriminating the vaccinated from infected animals. The data presented in this study are openly available in PRIDE data repository at https://www.ebi.ac.uk/pride/, reference number PXD022472.

Proteomic comparison of biofilm vs. planktonic Staphylococcus epidermidis cells suggests key metabolic differences between these conditions

Previous studies have shown that biofilm-forming bacteria are deficient in tricarboxylic acid (TCA) cycle metabolites, suggesting a relationship between these cellular processes. In this work, we compared the proteomes of planktonic vs biofilm cells from a clinical strain of Staphylococcus epidermidis using LC-MS/MS. A total of 168 proteins were identified from both growth conditions. The biofilm cells showed enrichment of proteins participating in glycolysis for the formation of pyruvate; however, the absence of TCA cycle proteins and the presence of lactate dehydrogenase, formate acetyltransferase, and acetoin reductase suggested that pyruvate was catabolized to their respective products: lactate, formate and acetoin. On the other hand, planktonic cells showed proteins participating in glycolysis and the TCA cycle, the pentose phosphate pathway, gluconeogenesis, ATP generation and the oxidative stress response. Functional networks with higher interconnection were predicted for planktonic proteins. We propose that in S. epidermidis, the relative absence of TCA cycle proteins is associated with the formation of biofilms and that lactate, formate and acetoin are the end products of partial glucose metabolism.

Phenotypic Modulation of Biofilm Formation in a Staphylococcus epidermidis Orthopedic Clinical Isolate Grown Under Different Mechanical Stimuli: Contribution From a Combined Proteomic Study

One of the major causes of prosthetic joint failure is infection. Recently, coagulase negative Staphylococcus epidermidis has been identified as an emergent, nosocomial pathogen involved in subclinical prosthetic joint infections (PJIs). The diagnosis of PJIs mediated by S. epidermidis is usually complex and difficult due to the absence of acute clinical signs derived from the host immune system response. Therefore, analysis of protein patterns in biofilm-producing S. epidermidis allows for the examination of the molecular basis of biofilm formation. Thus, in the present study, the proteome of a clinical isolate S. epidermidis was analyzed when cultured in its planktonic or sessile form to examine protein expression changes depending on culture conditions. After 24 h of culture, sessile bacteria exhibited increased gene expression for ribosomal activity and for production of proteins related to the initial attachment phase, involved in the capsular polysaccharide/adhesin, surface associated proteins and peptidoglycan biosynthesis. Likewise, planktonic S. epidermidis was able to aggregate after 24 h, synthesizing the accumulation associate protein and cell-wall molecules through the activation of the YycFG and ArlRS, two component regulatory pathways. Prolonged culture under vigorous agitation generated a stressful growing environment triggering aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. Further studies will be essential to support these findings in order to further delineate the complex mechanisms of biofilm formation of S. epidermidis and they could provide the groundwork for the development of new drugs against biofilm-related infections, as well as the identification of novel biomarkers of subclinical or chronic infections mediated by these emerging, low virulence pathogens.

A universal stress protein in Mycobacterium smegmatis sequesters the cAMP-regulated lysine acyltransferase and is essential for biofilm formation

Universal stress proteins (USPs) are present in many bacteria, and their expression is enhanced under various environmental stresses. We have previously identified a USP in Mycobacterium smegmatis that is a product of the msmeg_4207 gene and is a substrate for a cAMP-regulated protein lysine acyltransferase (KATms; MSMEG_5458). Here, we explored the role of this USP (USP4207) in M. smegmatis and found that its gene is present in an operon that also contains genes predicted to encode a putative tripartite tricarboxylate transporter (TTT). Transcription of the TTT-usp4207 operon was induced in the presence of citrate and tartrate, perhaps by the activity of a divergent histidine kinase-response regulator gene pair. A usp4207-deleted strain had rough colony morphology and reduced biofilm formation compared with the WT strain; however, both normal colony morphology and biofilm formation were restored in a Δusp4207Δkatms strain. We identified several proteins whose acetylation was lost in the Δkatms strain, and whose transcript levels increased in M. smegmatis biofilms along with that of USP4207, suggesting that USP4207 insulates KATms from its other substrates in the cell. We propose that USP4207 sequesters KATms from diverse substrates whose activities are down-regulated by acylation but are required for biofilm formation, thus providing a defined role for this USP in mycobacterial physiology and stress responses.

Antimicrobial Effects of Conditioned Medium From Amniotic Progenitor Cells in vitro and in vivo: Toward Tissue Regenerative Therapies for Bovine Mastitis

There is increasing evidence to suggest that, in addition to their regenerative effect, mesenchymal stromal cells (MSCs), and their secretome have an anti-inflammatory and antimicrobial role in the innate immune response in conditions such as sepsis. However, there is no published information on the effect of MSCs in bovine mastitis. Mastitis often results in extensive tissue damage due to multi-microorganism co-infection. This study investigated the ability of amniotic-derived conditioned medium (CM), in vitro and in vivo, to counteract microbial action and restore healthy tissue capable of milk production. Following determination of a dose–response curve, 10,000 colony-forming units (CFU) of Staphylococcus aureus (S. aureus) were inoculated into bovine mammary epithelial cell culture with and without 10% CM (supplemented either at the time of bacteria inoculation or after 4 h). Acridine orange staining was used to assess cell viability/apoptosis. Additionally, an in vivo study was performed using 48 dairy cows with acute and chronic mastitis, treated with CM (treated group) or antibiotics (control group). In vitro results showed that CM can attenuate bacterial growth, as evaluated by the number of CFU. After 24 h of culture with S. aureus, 89.67% of mammary epithelial cells treated with CM were still alive, whereas all cells cultured without CM were dead. Rates of epithelial cell survival (60.67%) were similar when CM was added 4 h after bacteria inoculation. There was no difference in somatic cell count between cases of acute mastitis in the CM-treated or control group in the in vivo study. However, relapses in chronic mastitis were less common in the group receiving CM. Our results show that CM is able to mitigate bacterial growth in vitro and may be particularly useful in the treatment of chronic mastitis, aiding restoration of milk production in cows that would otherwise be removed from the production cycle.