Deferred Growth Inhibition Assay to Quantify the Effect of Bacteria-derived Antimicrobials on Competition

Whole genome sequencing and characterization of Corynebacterium isolated from the healthy and dry eye ocular surface

BACKGROUND

The purpose of this study was to characterize Corynebacterium isolated from the ocular surface of dry eye disease patients and healthy controls. We aimed to investigate the pathogenic potential of these isolates in relation to ocular surface health. To this end, we performed whole genome sequencing in combination with biochemical, enzymatic, and antibiotic susceptibility tests. In addition, we employed deferred growth inhibition assays to examine how Corynebacterium isolates may impact the growth of potentially competing microorganisms including the ocular pathogens Pseudomonas aeruginosa and Staphylococcus aureus, as well as other Corynebacterium present on the eye.

RESULTS

The 23 isolates were found to belong to 8 different species of Corynebacterium with genomes ranging from 2.12 mega base pairs in a novel Corynebacterium sp. to 2.65 mega base pairs in C. bovis. Whole genome sequencing revealed the presence of a range of antimicrobial targets present in all isolates. Pangenome analysis showed the presence of 516 core genes and that the pangenome is open. Phenotypic characterization showed variously urease, lipase, mucinase, protease and DNase activity in some isolates. Attention was particularly drawn to a potentially new or novel Corynebacterium species which had the smallest genome, and which produced a range of hydrolytic enzymes. Strikingly the isolate inhibited in vitro the growth of a range of possible pathogenic bacteria as well as other Corynebacterium isolates. The majority of Corynebacterium species included in this study did not seem to possess canonical pathogenic activity.

CONCLUSIONS

This study is the first reported genomic and biochemical characterization of ocular Corynebacterium. A number of potential virulence factors were identified which may have direct relevance for ocular health and contribute to the finding of our previous report on the ocular microbiome, where it was shown that DNA libraries were often dominated by members of this genus. Particularly interesting in this regard was the observation that some Corynebacterium, particularly new or novel Corynebacterium sp. can inhibit the growth of other ocular Corynebacterium as well as known pathogens of the eye.

Direct Detection of Antibacterial-Producing Soil Isolates Utilizing a Novel High-Throughput Screening Assay

The ever-increasing global threat of common infections developing resistance to current therapeutics is rapidly accelerating the onset of a primitive post-antibiotic era in medicine. The prevention of further antimicrobial resistance development is unlikely due to the continued misuse of antibiotics, augmented by the lack of discovery of novel antibiotics. Screening large libraries of synthetic compounds have yet to offer effective replacements for current antibiotics. Due to historical successes, discovery from large and diverse natural sources and, more specifically, environmental bacteria, may still yield novel alternative antibiotics. However, the process of antibiotic discovery from natural sources is laborious and time-consuming as a result of outdated methodologies. Therefore, we have developed a simple and rapid preliminary screening assay to identify antibacterial-producing bacteria from natural sources. In brief, the assay utilizes the presence or absence of luminescence in bioluminescent reporter bacteria and test bacterium co-cultures in a 96-well plate format to determine the absence or presence of antibacterial compound production. Our assay, called the bioluminescent simultaneous antagonism (BSLA) assay, can accurately distinguish between known antibacterial-producing and non-producing test bacteria. The BSLA assay was validated by screening 264 unknown soil isolates which resulted in the identification of 10 antibacterial-producing isolates, effectively decreasing the pool of isolates for downstream analysis by 96%. By design, the assay is simple and requires only general laboratory equipment; however, we have shown that the assay can be scaled to automated high-throughput screening systems. Taken together, the BSLA assay allows for the rapid pre-screening of unknown bacterial isolates which, when coupled with innovative downstream dereplication and identification technologies, can effectively fast-track antimicrobial discovery.

Staphylococcus aureus in Substrates for Black Soldier Fly Larvae (Hermetia illucens) and Its Dynamics during Rearing

Black soldier fly larvae (BSFL; Hermetia illucens) are promising insects for the conversion of organic waste streams into valuable biomolecules. Such waste streams can contain foodborne pathogens. To assess this risk factor, this study evaluated the presence of Staphylococcus aureus in waste streams as a substrate ingredient for BSFL production as well as in the rearing process. First, the general microbiological quality and the occurrence of S. aureus were investigated for different waste streams. Staphylococcus aureus was abundantly present. Control of pH and water activity should avoid pathogens, which cannot grow in single-substrate ingredients, redeveloping when mixing streams for optimal substrate conditions for BSFL production. Next, it was investigated whether S. aureus present in the substrate was ingested and/or eradicated by BSFL. In inoculation trials, with S. aureus added to chicken feed as the substrate at 3 or 7 log CFU/g, the larvae showed a reducing effect on S. aureus. After 6 days, S. aureus counts were below the detection limit (2.0 log CFU/g) in all larvae samples and decreased in the substrate to <2.0 and <3.1 log CFU/g for inoculation levels of 3 and 7 log CFU/g, respectively. While this is promising, it is still recommended to monitor and control this pathogen in BSFL rearing. Intriguingly, screening of antimicrobial activity of dominant microorganisms associated with BSFL showed a clear activity of Trichosporon isolates against S. aureus. Future research should explore whether Trichosporon, which is frequently observed in BSFL, plays a role in controlling specific microorganisms, such as S. aureus. IMPORTANCE Given the increasing need for (more sustainable) methods to upcycle organic waste streams, the interest to rear insects, like black soldier fly larvae (BSFL), on such streams is increasing. This study reveals that S. aureus is abundantly present in such waste streams, which might be a point of attention for insect producers. At the same time, it reveals that when S. aureus was inoculated in chicken feed as the substrate, it was not detected in the larvae and was reduced in the substrate after 6 days. Future inoculation trials should investigate whether this reduction is substrate dependent or not. Toward the future, the role of the BSFL microbiota in controlling intestinal bacterial community homeostasis should be explored, because one of the dominant microorganisms associated with BSFL, Trichosporon spp., showed clear activity against S. aureus.

Corynebacterium accolens Has Antimicrobial Activity against Staphylococcus aureus and Methicillin-Resistant S. aureus Pathogens Isolated from the Sinonasal Niche of Chronic Rhinosinusitis Patients

Corynebacterium accolens is the predominant species of the healthy human nasal microbiota, and its relative abundance is decreased in the context of chronic rhinosinusitis (CRS). This study aimed to evaluate the antimicrobial potential of C. accolens isolated from a healthy human nasal cavity against planktonic and biofilm growth of Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) clinical isolates (CIs) from CRS patients. Nasal swabs from twenty non-CRS control subjects were screened for the presence of C. accolens using microbiological and molecular techniques. C. accolens CIs and their culture supernatants were tested for their antimicrobial activity against eight S. aureus and eight MRSA 4CIs and S. aureus ATCC25923. The anti-biofilm potential of C. accolens cell-free culture supernatants (CFCSs) on S. aureus biofilms was also assessed. Of the 20 nasal swabs, 10 C. accolens CIs were identified and confirmed with rpoB gene sequencing. All isolates showed variable antimicrobial activity against eight out of 8 S. aureus and seven out of eight MRSA CIs. Culture supernatants from all C. accolens CIs exhibited a significant dose-dependent antibacterial activity (p < 0.05) against five out of five representative S. aureus and MRSA CIs. This inhibition was abolished after proteinase K treatment. C. accolens supernatants induced a significant reduction in metabolic activity and biofilm biomass of S. aureus and MRSA CIs compared to untreated growth control (p < 0.05). C. accolens exhibited antimicrobial activity against S. aureus and MRSA CIs in both planktonic and biofilm forms and holds promise for the development of innovative probiotic therapies to promote sinus health.

From Microbial Dynamics to Functionality in the Rhizosphere: A Systematic Review of the Opportunities With Synthetic Microbial Communities

Synthetic microbial communities (SynComs) are a useful tool for a more realistic understanding of the outcomes of multiple biotic interactions where microbes, plants, and the environment are players in time and space of a multidimensional and complex system. Toward a more in-depth overview of the knowledge that has been achieved using SynComs in the rhizosphere, a systematic review of the literature on SynComs was performed to identify the overall rationale, design criteria, experimental procedures, and outcomes of in vitro or in planta tests using this strategy. After an extensive bibliography search and a specific selection process, a total of 30 articles were chosen for further analysis, grouping them by their reported SynCom size. The reported SynComs were constituted with a highly variable number of members, ranging from 3 to 190 strains, with a total of 1,393 bacterial isolates, where the three most represented phyla were Proteobacteria, Actinobacteria, and Firmicutes. Only four articles did not reference experiments with SynCom on plants, as they considered only microbial in vitro studies, whereas the others chose different plant models and plant-growth systems; some of them are described and reviewed in this article. Besides, a discussion on different approaches (bottom-up and top-down) to study the microbiome role in the rhizosphere is provided, highlighting how SynComs are an effective system to connect and fill some knowledge gaps and to have a better understanding of the mechanisms governing these multiple interactions. Although the SynCom approach is already helpful and has a promising future, more systematic and standardized studies are needed to harness its full potential.

Cultivable microbiota associated with Aurelia aurita and Mnemiopsis leidyi

The associated microbiota of marine invertebrates plays an important role to the host in relation to fitness, health, and homeostasis. Cooperative and competitive interactions between bacteria, due to release of, for example, antibacterial substances and quorum sensing (QS)/quorum quenching (QQ) molecules, ultimately affect the establishment and dynamics of the associated microbial community. Aiming to address interspecies competition of cultivable microbes associated with emerging model species of the basal animal phyla Cnidaria (Aurelia aurita) and Ctenophora (Mnemiopsis leidyi), we performed a classical isolation approach. Overall, 84 bacteria were isolated from A. aurita medusae and polyps, 64 bacteria from M. leidyi, and 83 bacteria from ambient seawater, followed by taxonomically classification by 16S rRNA gene analysis. The results show that A. aurita and M. leidyi harbor a cultivable core microbiome consisting of typical marine ubiquitous bacteria also found in the ambient seawater. However, several bacteria were restricted to one host suggesting host‐specific microbial community patterns. Interbacterial interactions were assessed by (a) a growth inhibition assay and (b) QS interference screening assay. Out of 231 isolates, 4 bacterial isolates inhibited growth of 17 isolates on agar plates. Moreover, 121 of the 231 isolates showed QS‐interfering activities. They interfered with the acyl‐homoserine lactone (AHL)‐based communication, of which 21 showed simultaneous interference with autoinducer 2. Overall, this study provides insights into the cultivable part of the microbiota associated with two environmentally important marine non‐model organisms and into interbacterial interactions, which are most likely considerably involved in shaping a healthy and resilient microbiota.

Evidence of Biocontrol Activity of Bioinoculants Against a Human Pathogen, Listeria monocytogenes

Due to rhizodeposits and various microbial interactions, the rhizosphere is an extremely dynamic system, which provides a conductive niche not only for bacteria beneficial to plants but also for those that might pose a potential threat to humans. The importance of bioinoculants as biocontrol agents to combat phytopathogens has been widely recognized. However, little information exists with respect to their role in inhibiting human pathogens in the rhizosphere. The present study is an attempt to understand the impact of an established bacterial consortium, Azotobacter chroococcum, Bacillus megaterium, and Pseudomonas fluorescens, on the survivability of Listeria monocytogenes in the rhizosphere of Cajanus cajan and Festuca arundinacea. An experiment conducted in Hoagland's medium in the presence of C. cajan demonstrated that the presence of bioinoculants impaired growth of L. monocytogenes compared to that observed in their absence. On the other hand, in the presence of F. arundinacea, no significant differences were observed in the population dynamics of L. monocytogenes in the presence or absence of the bioinoculants. Agar plate assay through cross streak method revealed the inhibition of L. monocytogenes by bioinoculants. Potential bioactive compounds were identified by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). These results suggest that agricultural amendments can act as protective agents against human pathogens while enforcing plant growth promotion.

Development of a Robust and Quantitative High-Throughput Screening Method for Antibiotic Production in Bacterial Libraries

Over the past 30 years, there has been a dramatic rise in the number of infections caused by multidrug-resistant bacteria, which have proliferated due to the misuse and overuse of antibiotics. Over this same time period, however, there has also been a decline in the number of antibiotics with novel mechanisms of action coming to market. Therefore, there is a growing need for an increase in the speed at which new antibiotics are discovered and developed. Natural products produced by bacteria have been and continue to be a robust source of novel antibiotics; however, new and complementary methods for screening large bacterial libraries for novel antibiotic production are needed due to the current agar methods being limited in scope, time consuming, and prone to error. Herein, we describe a rapid, robust, and quantitative high-throughput liquid culture screening method for antibiotic production by bacteria. This method has the ability to screen both mono- and coculture mixtures of bacteria in vitro and be adapted to other phenotypic natural product analyses. Over 260 bacterial species were screened in monoculture, and 38 and 34% were found to produce antibiotics capable of inhibition of Staphylococcus aureus or Escherichia coli, respectively, with 8 and 4% being classified as strong producers (≥30% growth inhibition), respectively. Bacteria found to not produce antibiotics in monoculture were also screened in coculture using an adaptation of this method. Of the more than 270 cocultures screened, 14 and 30% were found to produce antibiotics capable of inhibition of S. aureus or E. coli, respectively. Of those bacteria found to produce antibiotics in monoculture, 43 bacteria were subjected to 16S rRNA sequencing and found to be majority Pseudomonas (37%), Serratia (19%), and Bacillus (14%) bacteria, but two novel producers, Herbaspirillum and Kluyvera, were also found.

A prostate derived commensal Staphylococcus epidermidis strain prevents and ameliorates induction of chronic prostatitis by UPEC infection

Chronic prostatitis/Chronic pelvic pain syndrome (CP/CPPS) is a common syndrome with limited therapies and an unknown etiology. Previously, our laboratory has defined a potential role for pathogenic infection in disease onset. Intra-urethral infection with a uropathogenic Escherichia coli strain isolated from a CP/CPPS patient, CP1, induces prostatic inflammation and tactile allodynia in mice. We have also demonstrated that a prostate specific Staphylococcus epidermidis bacterial isolate, NPI (non-pain inducing), from a healthy subject reduces pain and inflammation in an experimental autoimmune prostatitis (EAP) murine model. Here we focus on the interplay between these human isolates in the context of prostatitis development and resolution. NOD/ShiLtJ mice were inoculated with either NP1 or CP1, or combinations of both. Infection with CP1 induced pelvic tactile allodynia after 7 days, while NPI instillation alone induced no such response. Instillation with NPI 7 days following CP1 infection resolved pelvic tactile allodynia and prophylactic instillation 7 days prior to CPI infection prevented its onset. Prophylactic NPI instillation also prevented CP1 colonization of both prostate and bladder tissues. In vitro analyses revealed that CP1 and NPI do not directly inhibit the growth or invasive potential of one another. Immunological analyses revealed that specific markers associated with CP1-induced pelvic allodynia were decreased upon NPI treatment or repressed by prophylactic colonization. This study demonstrates that a commensal bacterial isolate can inhibit the colonization, pain responses, and immunological activation to uropathogenic bacteria, emphasizing the power of a healthy prostatic microflora in controlling health and disease.