Resident Bacterial Species Research Articles

Resource availability drives bacteria community resistance to pathogen invasion via altering bacterial pairwise interactions.

Microbial interactions within resident communities are a major determinant of resistance to pathogen invasion. Yet, interactions vary with environmental conditions, raising the question of how community composition and environments interactively shape invasion resistance. Here, we use resource availability (RA) as a model parameter altering the resistance of model bacterial communities to invasion by the plant pathogenic bacterium Ralstonia solanacearum. We found that at high RA, interactions between resident bacterial species were mainly driven by the direct antagonism, in terms of the means of invader inhibition. Consequently, the competitive resident communities with a higher production of antibacterial were invaded to a lesser degree than facilitative communities. At low RA, bacteria produced little direct antagonist potential, but facilitative communities reached a relatively higher community productivity, which showed higher resistance to pathogen invasion than competitive communities with lower productivities. This framework may lay the basis to understand complex microbial interactions and biological invasion as modulated by the dynamic changes of environmental resource availability.

Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in a murine model of PSC

ObjectiveConflicting microbiota data exist for primary sclerosing cholangitis (PSC) and experimental models. Goal: define the function of complex resident microbes and their association relevant to PSC patients by studying germ-free...

Characterization of Bacterial Community Structure Dynamics in a Rat Burn Wound Model Using 16S rRNA Gene Sequencing.

Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a nonvolatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

Harnessing Tissue Engineering Tools to Interrogate Host-Microbiota Crosstalk in Cancer.

SummaryRecent studies have begun to highlight the diverse and tumor-specific microbiomes across multiple cancer types. We believe this work raises the important question of whether the classical “Hallmarks of Cancer” should be expanded to include tumor microbiomes. To answer this question, the causal relationships and co-evolution of these microbiotic tumor ecosystems must be better understood. Because host-microbe interactions should be studied in a physiologically relevant context, animal models have been preferred. Yet these models are often poor mimics of human tumors and are difficult to interrogate at high spatiotemporal resolution. We believe that in vitro tissue engineered platforms could provide a powerful alternative approach that combines the high-resolution of in vitro studies with a high degree of physiological relevance. This review will focus on tissue engineered approaches to study host-microbe interactions and to establish their role as an emerging hallmark of cancer with potential as a therapeutic target.

Genomic plasticity of pathogenic Escherichia coli mediates d-serine tolerance via multiple adaptive mechanisms

The molecular environment of the host can have profound effects on the behavior of resident bacterial species. We recently established how the sensing and response of enterohemorrhagic Escherichia coli (EHEC) to d-serine (d-Ser) resulted in down-regulation of type 3 secretion system-dependent colonization, thereby avoiding unfavorable environments abundant in this toxic metabolite. However, this model ignores a key determinant of the success of bacterial pathogens, adaptive evolution. In this study, we have explored the adaptation of EHEC to d-Ser and its consequences for pathogenesis. We rapidly isolated multiple, independent, EHEC mutants whose growth was no longer compromised in the presence of d-Ser. Through a combination of whole-genome sequencing and transcriptomics, we showed that tolerance could be attributed to disruption of one of two d-Ser transporters and/or activation of a previously nonfunctional d-Ser deaminase. While the implication of cytoplasmic transport in d-Ser toxicity was unsurprising, disruption of a single transporter, CycA, was sufficient to completely overcome the repression of type 3 secretion system activity normally associated with exposure to d-Ser. Despite the fact that this reveals a mechanism by which evolution could drive a pathogen to colonize new niches, interrogation of sequenced E. coli O157:H7 genomes showed a high level of CycA conservation, highlighting a strong selective pressure for functionality. Collectively, these data show that CycA is a critically important conduit for d-Ser uptake that is central to the niche restriction of EHEC.

Local biotic interactions drive species-specific divergence in soil bacterial communities.

It is well accepted that environmental heterogeneity and dispersal are key factors determining soil bacterial community composition, yet little is known about the role of local biotic interactions. Here we address this issue with an abundance-manipulation experiment that was conducted in a semiarid grassland. We manually increased the abundance of six randomly chosen resident bacterial species in separate, closed, communities and allowed the communities to recover in situ for 1 year. The single episode of increase in the abundance of different species drove species-specific community divergence accompanied by a decline in local diversity. Four of the six added species caused a decrease in the abundance of their closely related species, suggesting an important role of interspecific competition in driving the observed community divergence. Our results also suggested a lack of effective population regulations to force the relative abundance of manipulated species to revert to original level, which would allow persistence of the divergence among soil bacterial communities. We concluded that biotic interactions were important in determining soil bacterial community composition, which could result in substantial variation in soil bacterial community composition in abiotically homogenous environment.

The Role of the Genitourinary Microbiome in Pediatric Urology: a Review

In this review, we highlight the effects of the microbiome on urologic diseases that affect the pediatric patient. Perturbations in the urinary microbiome have been shown to be associated with a number of urologic diseases affecting children, namely urinary tract infection, overactive bladder/urge urinary incontinence, and urolithiasis. Recently, improved cultivation and sequencing technologies have allowed for the discovery of a significant and diverse microbiome in the bladder, previously assumed to be sterile. Early studies aimed to identify the resident bacterial species and demonstrate the efficacy of sequencing and enhanced quantitative urine culture. More recently, research has sought to elucidate the association between the microbiome and urologic disease, as well as to demonstrate effects of manipulation of the microbiome on various urologic pathologies. With an improved appreciation for the impact of the urinary microbiome on urologic disease, researchers have begun to explore the impact of these resident bacteria in pediatric urology.

East Meets West: The Increasing Incidence of Inflammatory Bowel Disease in Asia as a Paradigm for Environmental Effects on the Pathogenesis of Immune-Mediated Disease

East Meets West: The Increasing Incidence of Inflammatory Bowel Disease in Asia as a Paradigm for Environmental Effects on the Pathogenesis of Immune-Mediated Disease

Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers.

Microbial symbionts living within animal guts are largely composed of resident bacterial species, forming communities that often provide benefits to the host. Gut microbiomes of adult honey bees (Apis mellifera) include core residents such as the betaproteobacterium Snodgrassella alvi, alongside transient parasites such as the protozoan Lotmaria passim To test how these species affect microbiome composition and host physiology, we administered S alvi and/or L passim inocula to newly emerged worker bees from four genetic backgrounds (GH) and reared them in normal (within hives) or stressed (protein-deficient, asocial) conditions. Microbiota acquired by normal bees were abundant but quantitatively differed across treatments, indicating treatment-associated dysbiosis. Pretreatment with S. alvi made normal bees more susceptible to L. passim and altered developmental and detoxification gene expression. Stressed bees were more susceptible to L. passim and were depauperate in core microbiota, yet supplementation with S. alvi did not alter this susceptibility. Microbiomes were generally more variable by GH in stressed bees, which also showed opposing and comparatively reduced modulation of gene expression responses to treatments compared with normal bees. These data provide experimental support for a link between altered gut microbiota and increased parasite and pathogen prevalence, as observed from honey bee colony collapse disorder.

Using Anti‐Fungal Bacteria to Contest Snake Fungal Disease

Often referred to as indicator species, amphibians and reptiles are abundant and vital in ecosystems across the world. However, across the globe there is a decrease in this abundance due to various factors. Many species are already critically endangered or on the brink of extinction. One of these factors is the spread of various fungal diseases.Ophidiomvces ophiodiicola, also known as Snake Fungal Disease (SFD), is a new fungi spreading and residing on the skin of snakes. Although SFD does not immediately harm the infected reptile, in combination with other disturbances or stressors SFD could pose a serious threat to the reptile populations infected. The geographic range and the quantity of SFD infections are relatively unknown. Through this research we strive to isolate a residential bacteria from either reptiles’ skin or gut that posses antifungal properties along with estimate the extent of SFD infections. The first phase of this project was to collect skin and fecal samples from 18 species of snakes and lizards from the southeastern and southwestern US. We will then perform DNA extraction and real time PCR to determine if Ophidiomvces ophiodiicola was present on the skin or in the gut of each animal. We will also isolate resident bacterial species from the skin and gut and perform in vitro challenge assays against the snake fungal pathogen to determine the probiotic antifungal effects of resident skin bacteria. Antifungal bacterial species could be used for future probiotic field based treatments of reptiles at risk of infection from Ophidiomvces ophiodiicola.

Characterization of CLA-producing Butyrivibrio spp. reveals strain-specific variations.

Conjugated Linoleic Acid (CLA), a fatty acid with high nutraceutical value is produced in rumen by resident bacterial species, especially Butyrivibrio spp. The present study was undertaken to examine the diversity of indigenous Butyrivibrio spp. from rumen liquor of Indian ruminants. The isolates were screened for their CLA production capability at different level of linoleic acid (LA) (0, 200, 400, 600, 800 μg/ml) at different time intervals (0, 2, 4, 6, 12, and 24 h). A total of more than 300 anaerobic cultures were isolated and 31 of them were identified as Butyrivibrio spp. based on morphological, biochemical and molecular characterization. Further, molecular characterization revealed that a large portion (67.7 %) of isolated Butyrivibrio belonged to Butyrivibrio fibrisolvens (B. fibrisolvens) species which is considered to be the most active bacteria amongst the rumen bacteria populace in terms of CLA production. Bacterial isolate VIII (strain 4a) showed highest CLA production ability (140.77 μg/ml) when incubated at 200 μg/ml LA for 2 h, which is 240 % higher than the isolate XXVII, Butyrivibrio proteoclasticus (B. proteoclasticus) showing lowest CLA production (57.28 μg/ml) amongst the screened isolates. It was evident from the observations recorded during the course of experiments that CLA production ability is strain specific and thus did not follow a single pattern. CLA production also varied with time of incubation and concentration of free linoleic acid supplemented in the growth medium. The results of these findings put forward a strain that is high CLA producer and can be further exploited as an additive for enhancing meat and milk quality in ruminants.

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic T reg Cell Homeostasis

Regulatory T cells (Tregs) that express the transcription factor Foxp3 are critical for regulating intestinal inflammation. Candidate microbe approaches have identified bacterial species and strain-specific molecules that can affect intestinal immune responses, including species that modulate Treg responses. Because neither all humans nor mice harbor the same bacterial strains, we posited that more prevalent factors exist that regulate the number and function of colonic Tregs. We determined that short-chain fatty acids, gut microbiota-derived bacterial fermentation products, regulate the size and function of the colonic Treg pool and protect against colitis in a Ffar2-dependent manner in mice. Our study reveals that a class of abundant microbial metabolites underlies adaptive immune microbiota coadaptation and promotes colonic homeostasis and health.

GENETIC AND MORPHOTYPIC HETEROGENEITY OF SWIMMING POOL BACTERIAL POPULATIONS

The populations of resident bacterial species of the swimming pool community such as Pseudomonas aeruginosa, Bacillus sp., Acinetobacter lwoffii and Pseudomonas alcaligenes were analyzed. All these species showed stable in time heterogeneity by spontaneous mutation frequency and biofilm forming ability. There was notably high occurrence of mutators in all investigated populations. Our results show high level of genetic plasticity and adaptivity under conditions of starvation and exposure to biocides.

An Experimental Test of Darwin’s Naturalization Hypothesis

One of the oldest ideas in invasion biology, known as Darwin's naturalization hypothesis, suggests that introduced species are more successful in communities in which their close relatives are absent. We conducted the first experimental test of this hypothesis in laboratory bacterial communities varying in phylogenetic relatedness between resident and invading species with and without a protist bacterivore. As predicted, invasion success increased with phylogenetic distance between the invading and the resident bacterial species in both the presence and the absence of protistan bacterivory. The frequency of successful invader establishment was best explained by average phylogenetic distance between the invader and all resident species, possibly indicating limitation by the availability of the unexploited niche (i.e., organic substances in the medium capable of supporting the invader growth); invader abundance was best explained by phylogenetic distance between the invader and its nearest resident relative, possibly indicating limitation by the availability of the unexploited optimal niche (i.e., the subset of organic substances supporting the best invader growth). These results were largely driven by one resident bacterium (a subspecies of Serratia marcescens) posting the strongest resistance to the alien bacterium (another subspecies of S. marcescens). Overall, our findings support phylogenetic relatedness as a useful predictor of species invasion success.

Lectin Histochemical Detection of Special Sugars on the Mucosal Surfaces of the Rat Alimentary Tract

Surfaces of the most luminal positions of mucosae are fundamental settlement sites of indigenous bacteria throughout the rat alimentary tract. In these positions, also epithelial cell-shedding sites, the special sugar expression in the glycocalyx is very important as it provides possible ligands of bacterial lectins for attachment to epithelial cells. Therefore, the sugar expression in glycocalyx of epithelial cells was lectin-histochemically surveyed using 21 lectins throughout the rat alimentary tract. From the tongue to the nonglandular part of the stomach, α-D-Man, α-D-Glc and α-D-GalNAc were detected on the surface of the keratinized stratified squamous epithelium. In the glandular part of the stomach, α-D-Man, β-D-Gal-4GlcNAc, D-Gal, D-GalNAc, D-GlcNAc, α-L-Fuc- α-D-Gal-β(1-4)GlcNAc and bisected triantennary N-glycans were detected on the surface of gastric superficial epithelial cells. From the duodenum to the ileum, (GlcNAc)(2-4) was expressed exclusively on the epithelial cells in the apical portions of the intestinal villi. From the cecum to the rectum, α-D-Man, β-D-Gal-4GlcNAc, D-Gal, D-GalNAc, α-D-Gal(1-3)D-GalNAc, (GalNAc)(n) and NeuNAc were expressed on the intestinal superficial epithelial cells. These results suggest that special sugars are expressed on the most luminal portions of mucosae as exclusive epithelial cell-shedding sites, and that sugar expression differs among the various segments of the alimentary tract. These site differences might reflect differences in resident bacterial species in the rat alimentary tract.

Rapidly Growing Mycobacteria: Emerging Pathogens in Cosmetic Procedures of the Skin

The human skin is a rich environment of microorganisms, containing 10–50 million bacteria per square centimeter and 11000 species [1]. The skin forms an effective barrier, preventing invasion not only by resident bacterial species but also by pathogens that are transiently residing on the skin [2]. Thus, trauma, skin diseases, or surgical procedures that affect skin integrity are the main mechanism of entry for cutaneous infections, and these usually involve bacteria, such as streptococci and staphylococci. In cosmetic skin procedures, especially those involving subcutaneous injection of substances that are kept in vials that are used repeatedly over time, rapidly growing mycobacteria (RGM) have emerged as pathogens that cause outbreaks of skin and soft-tissue infection [3–5]. In this issue of Clinical Infectious Diseases, Regnier et al [3] report an outbreak of mycobacterial infection in Paris, France, that involved 16 patients who presented with painful, erythematous, draining subcutaneous nodules at the site of mesother-

The Gut Microbiota: A Microbial Arsenal Protecting Us From Infectious and Radiation-Induced Diarrhea

The Gut Microbiota: A Microbial Arsenal Protecting Us From Infectious and Radiation-Induced Diarrhea

Transcriptional Analysis and Functional Characterization of a Gene Pair Encoding Iron-Regulated Xenocin and Immunity Proteins of Xenorhabdus nematophila

We describe a two-gene cluster encoding a bacteriocin, xenocin, and the cognate immunity protein in the insect-pathogenic bacterium Xenorhabdus nematophila, which infects and kills larval stages of the common crop pest Helicoverpa armigera. The two genes, xcinA and ximB, are present in the genome as a single transcriptional unit, which is regulated under SOS conditions. The stress-inducible promoter was activated by mitomycin C, glucose, and Fe(3+) depletion and at an elevated temperature when it was tested in Escherichia coli cells. Expression of the xenocin protein alone in E. coli inhibited the growth of this organism. The growth inhibition was abolished when the immunity protein was also present. A recombinant xenocin-immunity protein complex inhibited the growth of E. coli indicator cells when it was added exogenously to a growing culture. Xenocin is an endoribonuclease with an enzymatically active C-terminal domain. Six resident bacterial species (i.e., Bacillus, Enterobacter, Enterococcus, Citrobacter, Serratia, and Stenotrophomonas species) from the H. armigera gut exhibited sensitivity to recombinant xenocin when the organisms were grown under iron-depleted conditions and at a high temperature. Xenocin also inhibited the growth of two Xenorhabdus isolates. This study demonstrates that Fe(3+) depletion acts as a common cue for synthesis of xenocin by X. nematophila and sensitization of the target strains to the bacteriocin.

Multiple bacterial species reside in chronic wounds: a longitudinal study

The aim of the study was to investigate the bacterial profile of chronic venous leg ulcers and the importance of the profile to ulcer development. Patients with persisting venous leg ulcers were included and followed for 8 weeks. Every second week, ulcer samples were collected and the bacterial species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus species (41.3%) and anaerobic bacteria (39.1%). Resident bacterial species were present in all the ulcers. In 76% of the ulcers, two or more (up to five) resident bacterial species were found. The most common resident bacterial species were S. aureus and P. aeruginosa. Furthermore, ulcers with P. aeruginosa were found to be significantly larger than ulcers without the presence of P. aeruginosa (P < 0.005). Our study demonstrated that the chronic wound is colonised by multiple bacterial species and that once they are established many of them persist in the wound. Our results suggest that the presence of P. aeruginosa in venous leg ulcers can induce ulcer enlargement and/or cause delayed healing.

The microbial flora in venous leg ulcers without clinical signs of infection. Repeated culture using a validated standardised microbiological technique.

The change of ulcer size in relation to the presence of species and quantities of microorganisms was analysed in 58 patients with venous leg ulcers, all without clinical signs of infection. Microbiological samples were taken on the day of inclusion and then repeated 4 times at monthly intervals or until the ulcer had healed or was too small to be cultured from. There was growth of microorganisms in all ulcers, and the numbers were below 10(4) per mm2 of ulcer surface in all cases. No correlation was found between ulcer size change and the species and amounts of microorganisms. Sixty-nine species were isolated. Staphylococcus aureus was found in 88%, Enterococcus faecalis in 74%, Enterobacter cloacae and Peptococcus magnus in 29%, and fungi in 11% of the samples. One or more obligate anaerobe species was found in 41% of the samples and in half of the ulcers and constituted 62% of all bacterial species. The colonising ulcer flora was markedly constant over time in the individual ulcers regardless of change in size. Resident bacterial species were found in 57 of the 58 ulcers. If all samples were considered, the microorganisms were associated with not more than one fifth of the variability in healing rate, as shown by linear multiple regression analysis. The same species of microorganisms were found in ulcers that decreased (or healed) and in those that increased in size. Although an association between the microorganisms and ulcer healing could not be ruled out in this study, there seems to be no indication for routinely performed culture in the absence of clinical signs of infection in venous leg ulcers.