Role of human microflora in health and disease

An alternative pentose phosphate pathway in human gut bacteria for the degradation of C5 sugars in dietary fibers

The microbial degradation of pentoses in the human gut is a crucial factor for the utilization of plant-based dietary fibers. A vast majority of gut microbes are able to use these C5-sugars as a carbon and energy source. However, the underlying metabolic pathways are not fully understood. Bioinformatic analysis showed that a large number of abundant gut bacteria lack genes encoding a transaldolase as a key enzyme of the pentose phosphate pathway. Among them was the important human gut microbe Prevotella copri, which was able to grow in minimal media containing xylose or hemicelluloses as the sole carbon source. Therefore, we looked for an alternative pathway for pentose conversion in P. copri using bioinformatics, enzyme activity assays, and the detection of intermediates of pentose metabolism. It became evident that the organism converted C5-sugars via the sedoheptulose-1,7-bisphosphate pathway (SBPP) to connect pentose metabolism with glycolysis. To circumvent the transaldolase reaction, P. copri uses the combined catalysis of a pyrophosphate-dependent phosphofructokinase and a fructose-bisphosphate aldolase. Furthermore, we present strong evidence that the SBPP is widely distributed in important gut bacteria, including members of the phyla Bacteroides, Firmicutes, Proteobacteria, Verrucomicrobia, and Lentisphaerae.

Placental Microbial Colonization and Its Association With Pre-eclampsia

The existence and role of the microbiome in regulating physiological and pathophysiological conditions including metabolism, energy homeostasis, immune tolerance, behavior, obesity, diabetes, and cardiovascular-related diseases is of immense interest. It is now clear that the human placenta is not sterile, but rather colonized with microbes. The placental and vaginal microbiomes are distinct however, the placental microbiome is comparable with the oral microbiome, with a limited variation when compared with the gut microbiome. Pre-eclampsia (PE), a pregnancy-specific hypertensive disorder, remains the leading cause of maternal-fetal morbidity and mortality. This is largely due to the lack of a clear etiology of PE and consequently, diagnostic strategies, and treatment are sub-optimal. The present review focuses on the current understanding of the placental microbiome and its implication in the etiology of PE. It provides a perspective on the alteration of placental microbiome as a possible therapeutic approach in the prevention and management of PE.

No appendix necessary: Fecal transplants and antibiotics can resolve Clostridium difficile infection

The appendix has been hypothesized to protect the colon against Clostridium difficile infection (CDI) by providing a continuous source of commensal bacteria that crowd out the potentially unhealthy bacteria and/or by contributing to defensive immune dynamics. Here, a series of deterministic systems comprised of ordinary differential equations, which treat the system as an ecological community of microorganisms, model the dynamics of colon microbiome. The first model includes migration of commensal bacteria from the appendix to the gut, while the second model expands this to also include immune dynamics. Simulations and simple analytic techniques are used to explore dynamics under biologically relevant parameters values. Both models exhibited bistability with steady states of a healthy state and of fulminant CDI. However, we find that the appendix size was much too small for migration to affect the stability of the system. Both models affirm the use of fecal transplants in conjunction with antibiotic use for CDI treatment, while the second model also suggests that anti-inflammatory drugs may protect against CDI. Ultimately, in general neither the appendiceal migration rate of commensal microbiota nor the boost to antibody production could exert an appreciable impact on the stability of the system, thus failing to support the proposed protective role of the appendix against CDI.

Emodin via colonic irrigation modulates gut microbiota and reduces uremic toxins in rats with chronic kidney disease

Gut microbiota plays a dual role in chronic kidney disease (CKD) and is closely linked to production of uremic toxins. Strategies of reducing uremic toxins by targeting gut microbiota are emerging. It is known that Chinese medicine rhubarb enema can reduce uremic toxins and improve renal function. However, it remains unknown which ingredient or mechanism mediates its effect. Here we utilized a rat CKD model of 5/6 nephrectomy to evaluate the effect of emodin, a main ingredient of rhubarb, on gut microbiota and uremic toxins in CKD. Emodin was administered via colonic irrigation at 5ml (1mg/day) for four weeks. We found that emodin via colonic irrigation (ECI) altered levels of two important uremic toxins, urea and indoxyl sulfate (IS), and changed gut microbiota in rats with CKD. ECI remarkably reduced urea and IS and improved renal function. Pyrosequencing and Real-Time qPCR analyses revealed that ECI resumed the microbial balance from an abnormal status in CKD. We also demonstrated that ten genera were positively correlated with Urea while four genera exhibited the negative correlation. Moreover, three genera were positively correlated with IS. Therefore, emodin altered the gut microbiota structure. It reduced the number of harmful bacteria, such as Clostridium spp. that is positively correlated with both urea and IS, but augmented the number of beneficial bacteria, including Lactobacillus spp. that is negatively correlated with urea. Thus, changes in gut microbiota induced by emodin via colonic irrigation are closely associated with reduction in uremic toxins and mitigation of renal injury.

Neer Award 2017: A rapid method for detecting Propionibacterium acnes in surgical biopsy specimens from the shoulder

BACKGROUND

Propionibacterium (P) acnes infection of the shoulder after arthroplasty is a common and serious complication. Current detection methods for P acnes involve anaerobic cultures that require prolonged incubation periods (typically 7-14 days). We have developed a polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) approach that sensitively and specifically identifies P acnes in tissue specimens within a 24-hour period.

METHODS

Primers were designed to amplify a unique region of the 16S rRNA gene in P acnes that contained a unique HaeIII restriction enzyme site. PCR and RFLP analyses were optimized to detect P acnes DNA in in vitro cultures and in arthroscopic surgical biopsy specimens from patients with P acnes infections.

RESULTS

A 564 base-pair PCR amplicon was derived from all of the known P acnes strains. HaeIII digests of the amplicon yielded a restriction fragment pattern that was unique to P acnes. P acnes-specific amplicons were detected in as few as 10 bacterial cells and in clinical biopsy specimens of infected shoulder tissues.

CONCLUSION

This PCR-RFLP assay combines the sensitivity of PCR with the specificity of RFLP mapping to identify P acnes in surgical isolates. The assay is robust and rapid, and a P acnes-positive tissue specimen can be confirmed within 24 hours of sampling, facilitating treatment decision making, targeted antibiotic therapy, and monitoring to minimize implant failure and revision surgery.

Marine Bivalve Mollusks As Possible Indicators of Multidrug-Resistant Escherichia coli and Other Species of the Enterobacteriaceae Family

The mechanisms for the development and spread of antibacterial resistance (ABR) in bacteria residing in environmental compartments, including the marine environment, are far from understood. The objective of this study was to examine the ABR rates in Escherichia coli and other Enterobacteriaceae isolates obtained from marine bivalve mollusks collected along the Norwegian coast during a period from October 2014 to November 2015. A total of 549 bivalve samples were examined by a five times three tube most probable number method for enumeration of E. coli in bivalves resulting in 199 isolates from the positive samples. These isolates were identified by biochemical reactions and matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry, showing that 90% were E. coli, while the remaining were species within the genera Klebsiella, Citrobacter, and Enterobacter. All 199 isolates recovered were susceptibility tested following the European Committee on Antimicrobial Susceptibility Testing disk diffusion method. In total, 75 of 199 (38%) isolates showed resistance to at least one antibacterial agent, while multidrug-resistance were seen in 9 (5%) isolates. One isolate conferred resistance toward 15 antibacterial agents. Among the 75 resistant isolates, resistance toward extended-spectrum penicillins (83%), aminoglycosides (16%), trimethoprim (13%), sulfonamides (11%), tetracyclines (8%), third-generation cephalosporins (7%), amphenicols (5%), nitrofurans (5%), and quinolones (5%), were observed. Whole-genome sequencing on a selection of 10 E. coli isolates identified the genes responsible for resistance, including bla_CTX-M genes. To indicate the potential for horizontal gene transfer, conjugation experiments were performed on the same selected isolates. Conjugative transfer of resistance was observed for six of the 10 E. coli isolates. In order to compare E. coli isolates from bivalves with clinical strains, multiple-locus variable number tandem repeats analysis (MLVA) was applied on a selection of 30 resistant E. coli isolates. The MLVA-profiles were associated with community-acquired E. coli strains causing bacteremia. Our study indicates that bivalves represent an important tool for monitoring antibacterial resistant E. coli and other members of the Enterobacteriaceae family in the coastal environment.

Bacterial Communities Differ among Drosophila melanogaster Populations and Affect Host Resistance against Parasitoids

In Drosophila, diet is considered a prominent factor shaping the associated bacterial community. However, the host population background (e.g. genotype, geographical origin and founder effects) is a factor that may also exert a significant influence and is often overlooked. To test for population background effects, we characterized the bacterial communities in larvae of six genetically differentiated and geographically distant D. melanogaster lines collected from natural populations across Europe. The diet for these six lines had been identical for ca. 50 generations, thus any differences in the composition of the microbiome originates from the host populations. We also investigated whether induced shifts in the microbiome-in this case by controlled antibiotic administration-alters the hosts' resistance to parasitism. Our data revealed a clear signature of population background on the diversity and composition of D. melanogaster microbiome that differed across lines, even after hosts had been maintained at the same diet and laboratory conditions for over 4 years. In particular, the number of bacterial OTUs per line ranged from 8 to 39 OTUs. Each line harboured 2 to 28 unique OTUs, and OTUs that were highly abundant in some lines were entirely missing in others. Moreover, we found that the response to antibiotic treatment differed among the lines and significantly altered the host resistance to the parasitoid Asobara tabida in one of the six lines. Wolbachia, a widespread intracellular endosymbiont associated with parasitoid resistance, was lacking in this line, suggesting that other components of the Drosophila microbiome caused a change in host resistance. Collectively, our results revealed that lines that originate from different population backgrounds show significant differences in the established Drosophila microbiome, outpacing the long-term effect of diet. Perturbations on these naturally assembled microbiomes to some degree influenced the hosts' resistance against natural parasites.

E. coli DH5α cell response to a sudden change in microfluidic chemical environment

Motile bacteria respond to changing chemical environment by moving towards or away from a particular location. Bacterial migration under chemical gradient is one of the most studied areas in biomedical field. In this work we looked into how bacterial cells respond to sudden change in the microfluidic chemical environment. E. coli DH5α cells were subjected to an attractant gradient (0.1 mM sorbitol--attractant to E. coli cells) and after 120 min the same cells were exposed to an inhibitor (0.1 mM NiSO4) gradient in the same microfluidic device. Our studies revealed that when the E. coli DH5α cells were exposed to 0.1 mM sorbitol, they showed faster chemotaxis towards the attractant (0.1 mM sorbitol) and achieved steady state by 60 min. When we replaced 0.1 mM sorbitol with 0.1 mM NiSO4 in the device we found that that the E. coli DH5α cells started responding to change in chemical environment within 10 min and achieved steady state at the end of 60 min. This shows that the bacterial cells respond to change in local chemical environment is within few minutes.

Deconjugated Bile Salts Produced by Extracellular Bile-Salt Hydrolase-Like Activities from the Probiotic Lactobacillus johnsonii La1 Inhibit Giardia duodenalis In vitro Growth

Giardiasis, currently considered a neglected disease, is caused by the intestinal protozoan parasite Giardia duodenalis and is widely spread in human as well as domestic and wild animals. The lack of appropriate medications and the spread of resistant parasite strains urgently call for the development of novel therapeutic strategies. Host microbiota or certain probiotic strains have the capacity to provide some protection against giardiasis. By combining biological and biochemical approaches, we have been able to decipher a molecular mechanism used by the probiotic strain Lactobacillus johnsonii La1 to prevent Giardia growth in vitro. We provide evidence that the supernatant of this strain contains active principle(s) not directly toxic to Giardia but able to convert non-toxic components of bile into components highly toxic to Giardia. By using bile acid profiling, these components were identified as deconjugated bile-salts. A bacterial bile-salt-hydrolase of commercial origin was able to mimic the properties of the supernatant. Mass spectrometric analysis of the bacterial supernatant identified two of the three bile-salt-hydrolases encoded in the genome of this probiotic strain. These observations document a possible mechanism by which L. johnsonii La1, by secreting, or releasing BSH-like activity(ies) in the vicinity of replicating Giardia in an environment where bile is present and abundant, can fight this parasite. This discovery has both fundamental and applied outcomes to fight giardiasis, based on local delivery of deconjugated bile salts, enzyme deconjugation of bile components, or natural or recombinant probiotic strains that secrete or release such deconjugating activities in a compartment where both bile salts and Giardia are present.

Effect of dual-type oligosaccharides on constipation in loperamide-treated rats

BACKGROUND/OBJECTIVES

Constipation is a condition that can result from intestinal deformation. Because humans have an upright posture, the effects of gravity can cause this shape deformation. Oligosaccharides are common prebiotics and their effects on bowel health are well known. However, studies of the physiological functionality of a product that contains both lactulose and galactooligosaccharides are insufficient. We investigated the constipation reduction effect of a dual-type oligosaccharide, Dual-Oligo, in loperamide-treated rats.

MATERIALS/METHODS

Dual-Oligo consists of galactooligosaccharides (15.80%) and lactulose (51.67%). Animals were randomly divided into four groups, the normal group (normal), control group (control), low concentration of Dual-Oligo (LDO) group, and high concentration of Dual-Oligo (HDO) group. After 7 days of oral administration, fecal pellet amount, fecal weight, water content of fecal were measured. Blood chemistry, short-chain fatty acid (SCFA), gastrointestinal transit ratio and length and intestinal mucosa were analyzed.

RESULTS

Dual-Oligo increased the fecal weight, and water content of feces in rats with loperamide-induced constipation. Gastrointestinal transit ratio and length and area of intestinal mucosa significantly increased after treatment with Dual-Oligo in loperamide-induced rats. A high concentration of Dual-Oligo tended to produce more acetic acid than that observed for the control group, and Dual-Oligo affected the production of total SCFA. Bifidobacteria concentration of cecal contents in the high-concentration oligosaccharide (HDO) and low-concentration oligosaccharide (LDO) groups was similar to the result of the normal group.

CONCLUSIONS

These results showed that Dual-Oligo is a functional material that is derived from a natural food product and is effective in ameliorating constipation.

Isolation of Propionibacterium acnes among the microbiota of primary endodontic infections with and without intraoral communication

Objectives

The presence of opportunistic pathogens such as Propionibacterium acnes (P. acnes) may contribute to the endodontic pathology. The presence of P. acnes may be influenced by different endodontic conditions.

The aims of the study were firstly, to identify P. acnes within the whole cultivable microbiota of primary endodontic infections, to investigate which P. acnes phylotypes predominate in such infections and secondly to determine if the presence of an “open” communication (e.g. a sinus) can be associated with the isolation of P. acnes from the root canal.

Material and methods

The predominant cultivable microbiota of 15 primary endodontic lesions (7 without communication with the oral environment and 8 with an open communication) were identified using partial 16S ribosomal RNA (rRNA) gene sequence analysis. The identification of the organism was determined by interrogating the Human Oral Microbiome Database. The P. acnes isolates were typed on the basis of the recA gene sequence comparison. A neighbor-joining tree was constructed using MEGA 4.1 with the inclusion of known recA sequences.

Results

There was no difference in the number of species identified from lesions without communication (5.86 ± 3.7) and those with communication (5.37 ± 3.6) (P > 0.05). PCR-based 16S rRNA gene sequencing revealed P. acnes as the most prevalent isolate recovered from lesions with communication. recA gene sequencing revealed two phylogenetic lineages present in lesion with communication, with mainly type I (further split into type IA and type IB) and type II.

Conclusions

The presence of P. acnes as opportunistic pathogens has been confirmed and may sustain the traits observed in specific clinical presentations.

Clinical relevance

Clinical management of open lesions may require further disinfection to eliminate opportunistic bacteria.

Propionibacterium acnes infection in shoulder arthroscopy patients with postoperative pain

BACKGROUND

Recent studies have identified Propionibacterium acnes as the causal organism in an increasing number of postoperative shoulder infections. Most reports have found a high rate of P acnes infection after open surgery, particularly shoulder arthroplasty. However, there are limited data regarding P acnes infections after shoulder arthroscopy.

MATERIALS AND METHODS

We prospectively collected data on all shoulder arthroscopies performed by the senior author from January 1, 2009, until April 1, 2013. Cultures were taken in all revision shoulder arthroscopy cases performed for pain, stiffness, or weakness. In addition, 2 cultures were taken from each of a cohort of 32 primary shoulder arthroscopy cases without concern for infection to determine the false-positive rate.

RESULTS

A total of 1,591 shoulder arthroscopies were performed during this period, 68 (4.3%) of which were revision procedures performed for pain, stiffness, or weakness. A total of 20 revision arthroscopies (29.4%) had positive culture findings, and 16 (23.5%) were positive for P acnes. In the control group, 1 patient (3.2%) had P acnes growth.

CONCLUSIONS

The rate of P acnes infection in patients undergoing revision shoulder arthroscopy is higher than previously published and should be considered in cases characterized by refractory postoperative pain and stiffness.

The magnitude and duration of Clostridium difficile infection risk associated with antibiotic therapy: a hospital cohort study

Antibiotic therapy is the principal risk factor for Clostridium difficile infection (CDI), but little is known about how risks cumulate over the course of therapy and abate after cessation. We prospectively identified CDI cases among adults hospitalized at a tertiary hospital between June 2010 and May 2012. Poisson regression models included covariates for time since admission, age, hospitalization history, disease pressure, and intensive care unit stay. Impacts of antibiotic use through time were modeled using 4 measures: current antibiotic receipt, time since most recent receipt, time since first receipt during a hospitalization, and duration of receipt. Over the 24-month study period, we identified 127 patients with new onset nosocomial CDI (incidence rate per 10,000 patient days [IR] = 5.86). Of the 4 measures, time since most recent receipt was the strongest independent predictor of CDI incidence. Relative to patients with no prior receipt of antibiotics in the last 30 days (IR = 2.95), the incidence rate of CDI was 2.41 times higher (95% confidence interval [CI] 1.41, 4.13) during antibiotic receipt and 2.16 times higher when patients had receipt in the prior 1–5 days (CI 1.17, 4.00). The incidence rates of CDI following 1–3, 4–6 and 7–11 days of antibiotic exposure were 1.60 (CI 0.85, 3.03), 2.27 (CI 1.24, 4.16) and 2.10 (CI 1.12, 3.94) times higher compared to no prior receipt. These findings are consistent with studies showing higher risk associated with longer antibiotic use in hospitalized patients, but suggest that the duration of increased risk is shorter than previously thought.

In vitro evaluation of the mucin-adhesion ability and probiotic potential of Lactobacillus mucosae LM1

AIMS

In this report, we characterized the probiotic potential of Lactobacillus mucosae LM1, focusing on its in vitro mucin-adhesion abilities.

METHODS AND RESULTS

Screening assays were used to evaluate LM1. Previous studies on Lact. mucosae species have been performed, but few have examined the ability of this species to adhere to and colonize the intestinal mucosa. Thus, adhesion, aggregation and pathogen inhibition assays of LM1 along with microbial adhesion to solvents (MATS) assay were carried out in comparison with another putative probiotic, Lactobacillus johnsonii PF01, and the commercial strain, Lactobacillus rhamnosus GG. Based on MATS assay, the cell surfaces of the lactobacilli strains were found to be hydrophobic and highly electron-donating, but the average hydropathy (GRAVY) index of predicted surface-exposed proteins in the LM1 genome indicated that most were hydrophilic. LM1 showed the highest adhesion, aggregation and hydrophobicity among the strains tested and significantly inhibited the adhesion of Escherichia coli K88 and Salmonella enterica serovar Typhimurium KCCM 40253. Correlations among adhesion, aggregation and hydrophobicity, as well as between coaggregation and displacement of E. coli, were observed.

CONCLUSIONS

Increased adhesion may not always correlate with increased pathogen inhibition due to various strain-specific mechanisms. Nevertheless, LM1 has promising probiotic properties that can be explored further using a genomics approach.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our data on adhesion of LM1 strain showed a significant correlation between adhesion, hydrophobicity of cell surface and autoaggregation. This study gives basic knowledge for the elucidation of the adhesion mechanism of Lactobacillus sp. and prediction of its adherence in specific host models.

Epidemiology of infections in cancer patients

Although major advances in the care of cancer patients over the past several decades have resulted in improved survival, infectious complications remain a significant cause of morbidity and mortality. To successfully identify, treat, and prevent infections, a comprehensive understanding of risk factors that predispose to infection and of commonly encountered pathogens is necessary. In addition, clinicians must keep abreast of the changing epidemiology of infections in this population. As therapeutic modalities continue to evolve, as established pathogens become increasingly drug resistant, and as new pathogens are discovered, successful management of infections will continue to present challenges in the years to come.

Microbiomes of unreactive and pathologically altered ileocecal lymph nodes of slaughter pigs

Microbe-laden dendritic cells are shifted to ileocecal lymph nodes (ICLNs), where microbes are concentrated and an adequate immune response is triggered. Hence, ICLNs are at a crucial position in immune anatomy and control processes of the local immune system. Pathological alterations in ICLNs, such as reactive hyperplasia, lymphadenitis purulenta, or granulomatosa, can harbor a multitude of pathogens and commensals, posing a potential zoonotic risk in animal production. The aim of this study was to characterize the microbial diversity of unreactive ICLNs of slaughter pigs and to investigate community shifts in reactive ICLNs altered by enlargement, purulence, or granulomatous formations. Pyrosequencing of 16S rRNA gene amplicons from 32 ICLNs yielded 175,313 sequences, clustering into 650 operational taxonomic units (OTUs). OTUs were assigned to 239 genera and 11 phyla. Besides a highly diverse bacterial community in ICLNs, we observed significant shifts in pathologically altered ICLNs. The relative abundances of Cloacibacterium- and Novosphingobium-associated OTUs and the genus Faecalibacterium were significantly higher in unreactive ICLNs than in pathologically altered ICLNs. Enlarged ICLNs harbored significantly more Lactobacillus- and Clostridium-associated sequences. Relative abundances of Mycoplasma, Bacteroides, Veillonella, and Variovorax OTUs were significantly increased in granulomatous ICLNs, whereas abundances of Pseudomonas, Escherichia, and Acinetobacter OTUs were significantly increased in purulent ICLNs (P < 0.05). Correlation-based networks revealed interactions among OTUs in all ICLN groups, and discriminant analyses depicted discrimination in response to pathological alterations. This study is the first community-based survey in ICLNs of livestock animals and will provide a basis to broaden the knowledge of microbe-host interactions in pigs.

Analysis of the human intestinal microbiota from 92 volunteers after ingestion of identical meals

The intestinal microbiota composition of 92 volunteers living in Japan was identified following the consumption of 'identical meals' (1,879 kcal/day) for 3 days. When faecal samples were analysed by terminal restriction fragment length polymorphism with several primer-restriction enzyme systems and then clustered, the patterns could be divided into 2 clusters. Contribution tests and partition modelling showed that OTU211 of the 35f-MspI system and OTU237 of the 35f-AluI system were key factors in the distribution of these groups. However, significant differences among these groups in terms of body mass index and age were not observed.

Looking at microbial metabolism by high-resolution (2)H-NMR spectroscopy

We analyzed the applicability of high-resolution ²H-HMR spectroscopy for the analysis of microbe metabolism in samples of mitochondrion isolated from rat liver and from aqueous extracts of homogenates of rat liver and other organs and tissues in the presence of high D₂O contents. Such analysis is possible due to the fast microbe adaptation to life in the heavy water. It is also shown that some enzymatic processes typical for the intact cells are preserved in the homogenized tissue preparations. The microbial and cellular metabolic processes can be differentiated via the strategic use of cell poisons and antibiotics.

Effects of green tea consumption on human fecal microbiota with special reference to Bifidobacterium species

Green tea is one of the most popular beverages in the world. Its beneficial health effects and components have been extensively reviewed. However, little is known about the influence of green tea consumption on the human intestinal microbiota (HIM), which plays a crucial role in human health. Ten volunteers who did not usually consume green tea, drank it for 10 days and then stopped drinking it for 7 days. Their fecal samples were collected at three time points: before beginning the 10-day green-tea regime, at the conclusion of that 10 days, and 7 days after stopping the regime. Their fecal samples were analyzed by terminal restriction fragment length polymorphism with specific primer-restriction enzyme systems for HIM and by using a real-time PCR method for the Bifidobacterium species. Although the HIM of each subject was relatively stable, the proportion of Bifidobacterium species played an important role in the classification of their fecal microbiota. Although there were inter-individual differences in the Bifidobacterium species, an overall tendency for the proportion of bifidobacteria to increase because of green tea consumption was noted. However, little change was observed in the composition of Bifidobacterium species in each sample. This suggests that the change in proportion was induced, not by an inter-species transition, but by an intra-species increase and/or decrease. In conclusion, green tea consumption might act as a prebiotic and improve the colon environment by increasing the proportion of the Bifidobacterium species.

Establishing a relationship between bacteria in the human gut and complex regional pain syndrome

Complex Regional Pain Syndrome (CRPS) is a serious and painful condition involving the peripheral and central nervous systems. Full comprehension of the disorder's pathophysiology remains incomplete, but research implicates the immune system as a contributor to chronic pain. Because of the impact gastrointestinal bacteria have in the development and behavior of the immune system, this study compares the GI microbial communities of 16 participants with CRPS (5 of whom have intestinal discomforts) and 16 healthy controls using 454 sequencing technology. CRPS subjects were found to have significantly less diversity than their healthy counterparts. Statistical analysis of the phylogenetic classifications revealed significantly increased levels of Proteobacteria and decreased levels of Firmicutes in CRPS subjects. Clustering analysis showed significant separation between healthy controls and CRPS subjects. These results support the hypothesis that the GI microbial communities of CRPS participants differ from those of their healthy counterparts. These variations may hold the key to understanding how CRPS develops and provide information that could yield a potential treatment.

Bacteria on catheters in patients undergoing peritoneal dialysis

BACKGROUND

Peritonitis is the leading cause of morbidity for peritoneal dialysis (PD) patients, and microbial biofilms have previously been identified on catheters from infected patients. However, few studies of catheters from patients without clinical signs of infection have been undertaken. The aim of the present study was to investigate the extent to which bacteria are present on catheters from PD patients with no symptoms of infection.

METHODS

Microbiologic culturing under aerobic and anaerobic conditions and confocal laser scanning microscopy were used to determine the distribution of bacteria on PD catheters from 15 patients without clinical signs of infection and on catheters from 2 infected patients. The 16S rRNA gene sequencing technique was used to identify cultured bacteria.

RESULTS

Bacteria were detected on 12 of the 15 catheters from patients without signs of infection and on the 2 catheters from infected patients. Single-species and mixed-microbial communities containing up to 5 species were present on both the inside and the outside along the whole length of the colonized catheters. The bacterial species most commonly found were the skin commensals Staphylococcus epidermidis and Propionibacterium acnes, followed by S. warneri and S. lugdunensis. The strains of these micro-organisms, particularly those of S. epidermidis, varied in phenotype with respect to their tolerance of the major classes of antibiotics.

CONCLUSIONS

Bacteria were common on catheters from patients without symptoms of infection. Up to 4 different bacterial species were found in close association and may represent a risk factor for the future development of peritonitis in patients hosting such micro-organisms.

Microbiology of the skin and the role of biofilms in infection

The integrity of human skin is central to the prevention of infection. Acute and chronic wounds can develop when the integrity of skin as a barrier to infection is disrupted. As a multi-functional organ, skin possesses important biochemical and physical properties that influence its microbiology. These properties include a slightly acidic pH, a low moisture content, a high lipid content (which results in increased hydrophobicity) and the presence of antimicrobial peptides. Such factors have a role to play in preventing exogenous microbial colonisation and subsequent infection. In addition, the properties of skin both select for and enhance colonisation and biofilm formation by certain 'beneficial' micro-organisms. These beneficial micro-organisms can provide further protection against colonisation by potential pathogens, a process known as colonisation resistance. The aim of this paper is to summarise the microflora of skin and wounds, highlighting the role of certain micro-organisms and biofilms in associated infections.

Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra

Nautella sp. R11, a member of the marine Roseobacter clade, causes a bleaching disease in the temperate-marine red macroalga, Delisea pulchra. To begin to elucidate the molecular mechanisms underpinning the ability of Nautella sp. R11 to colonize, invade and induce bleaching of D. pulchra, we sequenced and analyzed its genome. The genome encodes several factors such as adhesion mechanisms, systems for the transport of algal metabolites, enzymes that confer resistance to oxidative stress, cytolysins, and global regulatory mechanisms that may allow for the switch of Nautella sp. R11 to a pathogenic lifestyle. Many virulence effectors common in phytopathogenic bacteria are also found in the R11 genome, such as the plant hormone indole acetic acid, cellulose fibrils, succinoglycan and nodulation protein L. Comparative genomics with non-pathogenic Roseobacter strains and a newly identified pathogen, Phaeobacter sp. LSS9, revealed a patchy distribution of putative virulence factors in all genomes, but also led to the identification of a quorum sensing (QS) dependent transcriptional regulator that was unique to pathogenic Roseobacter strains. This observation supports the model that a combination of virulence factors and QS-dependent regulatory mechanisms enables indigenous members of the host alga's epiphytic microbial community to switch to a pathogenic lifestyle, especially under environmental conditions when innate host defence mechanisms are compromised.

Effect of Lactobacillus fermentum on beta2 toxin production by Clostridium perfringens

Clostridium perfringens, although a member of the normal gut flora, is also an important cause of intestinal disease in animals and, to a lesser extent, in humans. Disease is associated with the production of one or more toxins, and little is known about environmental influences on the production of these toxins. One of the health-promoting effects of lactic acid bacteria (LAB) is the establishment and maintenance of a low pH in the intestine since an acidic environment inhibits the growth of many potentially harmful bacteria. Here, the effect of the LAB Lactobacillus fermentum on beta2 toxin production by C. perfringens is described. Coculturing of C. perfringens with L. fermentum showed that under in vitro conditions, L. fermentum was capable of silencing beta2 toxin production by C. perfringens without influencing bacterial viability. The reduction in toxin production was shown to be most likely a result of the decline in pH. Quantitative PCR showed that the reduction in beta2 toxin production was due to a decrease in cpb2 mRNA. These results suggest that in the intestine, the production of beta2 toxin by C. perfringens might be regulated by other members of the normal intestinal flora.

How beneficial is the use of probiotic supplements for the aging gut?

The specific health benefits of probiotic supplementation in aging populations remain relatively undefined. Although some probiotic research performed to date has focused on specific populations – particular disease groups or those in dynamic life stages such as the very young and older adults – dedicated studies of older subjects with a typical range of age-related conditions are few. Published studies also feature a narrow range of probiotic strains. Exploitation of strain specificity to modulate the composition and function of the microbiota is crucial to maximize the potential benefit of probiotics. A combination of prebiotic (dietary) and probiotic agents may prove most effective in targeted modulation of the microbiota. The efficacy of specific probiotic strains in modulating the microbiota of older populations is worth pursuing, although the role of antibiotics and polypharmacy (use of multiple medications) in influencing the potential benefits of probiotic intervention requires more dedicated study.

Passive immunoprotection targeting a secreted CAMP factor of Propionibacterium acnes as a novel immunotherapeutic for acne vulgaris

Propionibacterium acnes (P. acnes) bacteria play a key role in the pathogenesis of acne vulgaris. Although our previous studies have demonstrated that vaccines targeting a surface sialidase or bacterial particles exhibit a preventive effect against P. acnes, the lack of therapeutic activities and incapability of neutralizing secretory virulence factors motivate us to generate novel immunotherapeutics. In this study, we develop an immunotherapeutic antibody to secretory Christie-Atkins-Munch-Peterson (CAMP) factor of P. acnes. Via agroinfiltration, P. acnes CAMP factor was encapsulated into the leaves of radishes. ICR mice intranasally immunized with whole leaves expressing CAMP factor successfully produced neutralizing antibodies that efficiently attenuated P. acnes-induced ear swelling and production of macrophage-inflammatory protein-2. Passive neutralization of CAMP factor enhanced immunity to eradicate P. acnes at the infection site without influencing bacterial growth elsewhere. We propose that CAMP factor is a novel therapeutic target for the treatment of various P. acnes-associated diseases and highlight the concept of neutralizing P. acnes virulence without disturbing the bacterial commensalism in human microbiome.

Staphylococcus aureus hijacks a skin commensal to intensify its virulence: immunization targeting β-hemolysin and CAMP factor

The need for a new anti-Staphylococcus aureus therapy that can effectively cripple bacterial infection, neutralize secretory virulence factors, and lower the risk of creating bacterial resistance is undisputed. Here, we propose what is, to our knowledge, a previously unreported infectious mechanism by which S. aureus may commandeer Propionibacterium acnes, a key member of the human skin microbiome, to spread its invasion and highlight two secretory virulence factors (S. aureus β-hemolysin and P. acnes CAMP (Christie, Atkins, Munch-Peterson) factor) as potential molecular targets for immunotherapy against S. aureus infection. Our data demonstrate that the hemolysis and cytolysis by S. aureus were noticeably augmented when S. aureus was grown with P. acnes. The augmentation was significantly abrogated when the P. acnes CAMP factor was neutralized or β-hemolysin of S. aureus was mutated. In addition, the hemolysis and cytolysis of recombinant β-hemolysin were markedly enhanced by recombinant CAMP factor. Furthermore, P. acnes exacerbated S. aureus-induced skin lesions in vivo. The combination of CAMP factor neutralization and β-hemolysin immunization cooperatively suppressed the skin lesions caused by coinfection of P. acnes and S. aureus. These observations suggest a previously unreported immunotherapy targeting the interaction of S. aureus with a skin commensal.

Role of probiotics in the prevention of the enteric colonization by Candida in preterm newborns: incidence of late-onset sepsis and neurological outcome

OBJECTIVE

To evaluate the efficacy of probiotics in the prevention of gastrointestinal colonization by Candida species, of late-onset sepsis and neurological outcome in preterm newborns.

STUDY DESIGN

A prospective study was conducted in 249 preterms who were subdivided into three groups: one group (n=83) was supplemented with Lactobacillus (L.) reuteri, one group with L. rhamnosus (n=83) and the other with no supplementation (n=83). The fungal colonization in the gastrointestinal tract, the late onset of sepsis and clinical parameters were recorded. A neurological structured assessment was further performed at 1 year of age.

RESULT

Candida stool colonization was significantly higher (P<0.01) in the control group than in the groups treated with probiotics. The L. reuteri group presented a significantly higher reduction in gastrointestinal symptoms than did the L. rhamnosus and control groups. Infants treated with probiotics showed a statistically significant lower incidence of abnormal neurological outcome than did the control group.

CONCLUSION

The use of both probiotics seems to be effective in the prevention of gastrointestinal colonization by Candida, in the protection from late-onset sepis and in reducing abnormal neurological outcomes in preterms.

Identification, cloning, heterologous expression, and characterization of a NADPH-dependent 7β-hydroxysteroid dehydrogenase from Collinsella aerofaciens

A gene encoding an NADPH-dependent 7β-hydroxysteroid dehydrogenase (7β-HSDH) from Collinsella aerofaciens DSM 3979 (ATCC 25986, formerly Eubacterium aerofaciens) was identified and cloned in this study. Sequence comparison of the translated amino acid sequence suggests that the enzyme belongs to the short-chain dehydrogenase superfamily. This enzyme was expressed in Escherichia coli with a yield of 330 mg (5,828 U) per liter of culture. The enzyme catalyzes both the oxidation of ursodeoxycholic acid (UDA) forming 7-keto-lithocholic acid (KLA) and the reduction of KLA forming UDA acid in the presence of NADP(+) or NADPH, respectively. In the presence of NADPH, 7β-HSDH can also reduce dehydrocholic acid. SDS-PAGE and gel filtration of the expressed and purified enzyme revealed a dimeric nature of 7β-HSDH with a size of 30 kDa for each subunit. If used for the oxidation of UDA, its pH optimum is between 9 and 10 whereas for the reduction of KLA and dehydrocholic acid it shows an optimum between pH 4 to 6. Usage of the enzyme for the biotransformation of KLA in a 0.5-g scale showed that this 7β-HSDH is a useful biocatalyst for producing UDA from suitable precursors in a preparative scale.

In vitro anaerobic biofilms of human colonic microbiota

The human gastrointestinal tract hosts a complex community of microorganisms that grow as biofilms on the intestinal mucosa. These bacterial communities are not well characterized, although they are known to play an important role in human health. This study aimed to develop a model for culturing biofilms (surface-adherent communities) of intestinal microbiota. The model utilizes adherent mucosal bacteria recovered from colonic biopsies to create multi-species biofilms. Culture on selective media and confocal microscopy indicated the biofilms were composed of a diverse community of bacteria. Molecular analyses confirmed that several phyla were represented in the model, and demonstrated stability of the community over 96 h when cultured in the device. This model is novel in its use of a multi-species community of mucosal bacteria grown in a biofilm mode of growth.

Propionibacterium acnes and Staphylococcus epidermidis isolated from refractory endodontic lesions are opportunistic pathogens

The predominant cultivable microbiota from 20 refractory endodontic lesions (9 with abscesses and 11 without abscesses) were determined, and Propionibacterium acnes and Staphylococcus epidermidis were among the most predominant organisms. The number of species identified from lesions with abscesses (14.1 ± 2.6) was significantly greater (P < 0.001) than the number from lesions without abscesses (7.4 ± 5.9). Comparison of perioral isolates using repetitive extragenic palindromic PCR of the same species from the same subjects demonstrated that the endodontic and skin populations were significantly different. The P. acnes isolates were typed on the basis of recA gene sequence comparison, and only three types (types I, II, and III) were identified among 125 isolates examined. However, we found that type I (type IA and IB) isolates were primarily isolated from the skin, while types II and III were significantly more likely to be isolated from the endodontic lesions (P < 10(-10)). We found that the robustness of the recA phylotypes was not strong by comparing the partial gene sequences of six putative virulence determinants, PAmce, PAp60, PA-25957, PA-5541, PA-21293, and PA-4687. The resulting neighbor-joining trees were incongruent, and significant (phi test; P = 2.2 × 10(-7)) evidence of recombination was demonstrated, with significant phylogenetic heterogeneity being apparent within the clusters. P. acnes and S. epidermidis isolated from refractory endodontic infections, with or without periapical abscesses, are likely to be nosocomial infections.

Cadmium chloride exhibits a profound toxic effect on bacterial microflora of the mice gastrointestinal tract

Cadmium (Cd²(+)), a naturally occurring heavy metal, is an important environmental pollutant and a potent toxicant to bacteria. The gastrointestinal (GI) tract microflora has a marked capacity to cope with the increased load of ingested metals. However, heavy metals may have harmful effects on GIT microflora. Under the conditions of experimental exposure to cadmium, changes in the population of intestinal microflora in healthy mice were examined. Five experimental groups received 23 to 50 mg kg⁻¹ cadmium in drinking water and control group was given water free from cadmium for 45 days. Intestinal contents and biopsy samples were aseptically collected and bacterial counts were performed. The microflora of the intestine in control group was represented by bacteria of the genera Bacillus cereus, Lactobacillus spp., Clostridium spp., Escherichia coli, Klebsiella spp., Pseudomonas spp., Enterococcus spp. and Proteus spp. As the result of dysbiosis induced by the introduction of cadmium, a sharp decrease in the population of all microbial species in the intestine was observed. The deleterious effect of cadmium appeared to be less in the large intestine and rectum than that of small intestine, suggesting a site-specific influence of cadmium. The gram-negative bacteria tested were less sensitive to cadmium compared to the gram-positive bacteria because of their possible different ability to uptake the metal ions.

The role of infection in the aetiology of inflammatory bowel disease

We have greatly increased our understanding of the genetics of inflammatory bowel disease (IBD) in the last decade; however, migrant studies highlight the importance of environment in disease risk. The possibility that IBD is an infection has been debated since the first description of Crohn's disease. Mycobacterium avium paratuberculosis was the first organism to be suggested as an IBD pathogen, and it has been argued that it fulfils Koch's postulates and could be designated the cause of Crohn's disease. Other organisms have been postulated as possible IBD pathogens, including various Helicobacter species, one of which has been identified in primate colitis;others are widely used in animal models of IBD. Adherent invasive Escherichia coli appear specific to ileal Crohn's disease and have been shown to induce the release of TNF-alpha, a key cytokine in IBD inflammation. The aim of this article is to give a concise overview of the infections postulated as being relevant to the onset of IBD. We will also briefly cover the immunology underpinning IBD, in addition to reviewing current knowledge regarding other microorganisms that are associated with modifying the risk of developing IBD. It may be that infectious organisms have an orchestrator role in the development of dysbiosis and subsequently IBD.

Heterologous CD8 T cell immune response to HSV induced by toll like receptor ligands

A memory response is established following primary antigen exposure that stays more or less constant. It appears to adopt a set-point in magnitude but upon re-exposure the response is quicker and better and there is an upward shift in memory frequency that varies with individuals based on the exposure pattern to other microbes or its components. Our investigations were designed to test such differences of non-specific stimulation by PAMPs in lowering the threshold of activation. Neonatal mice were pre-exposed to TLR-ligands intermittently and later analyzed for its resilience to challenge with virus during adult-life. Secondly, adult mice with pre-existing memory to virus were exposed to various TLR-ligands and analyzed for their quality of memory response. The TLR-ligands exposed animals were better responders to a new agent exposure compared to the animals kept in sterile surroundings. Moreover, immune memory recall and the viral specific CD8(+) T cells response with TLR-ligands were comparable to the recall response with the cognate antigen. The results provide insights into the role of hyper-sanitized environment versus PAMPs mediated signaling in adaptive immunity and long-term immune memory.

NMR-based metabonomics analysis of mouse urine and fecal extracts following oral treatment with the broad-spectrum antibiotic enrofloxacin (Baytril)

The human gastrointestinal tract is home to hundreds of species of bacteria and the balance between beneficial and pathogenic bacteria plays a critical role in human health and disease. The human infant, however, is born with a sterile gut and the complex gastrointestinal host/bacterial ecosystem is only established after birth by rapid bacterial colonization. Composition of newborn gut flora depends on several factors including type of birth (Ceasarian or natural), manner of early feeding (breast milk or formula), and exposure to local, physical environment. Imbalance in normal, healthy gut flora contributes to several adult human diseases including inflammatory bowel (ulcerative colitis and Crohn's disease) and Clostridium difficile associated disease, and early childhood diseases such as necrotizing enterocolitis. As a first step towards characterization of the role of gut bacteria in human health and disease, we conducted an 850 MHz (1)H nuclear magnetic resonance spectroscopy study to monitor changes in metabolic profiles of urine and fecal extracts of 15 mice following gut sterilization by the broad-spectrum antibiotic enrofloxacin (also known as Baytril). Ten metabolites changed in urine following enrofloxacin treatment including decreased acetate due to loss of microbial catabolism of sugars and polysaccharides, decreased trimethylamine-N-oxide due to loss of microbial catabolism of choline, and increased creatine and creatinine due to loss of microbial enzyme degradation. Eight metabolites changed in fecal extracts of mice treated with enrofloxacin including depletion of amino acids produced by microbial proteases, reduction in metabolites generated by lactate-utilizing bacteria, and increased urea caused by loss of microbial ureases.

Probiotics and prebiotics in infant nutrition

The human colonic microflora has a central role in health and disease, being unique in its complexity and range of functions. As such, dietary modulation is important for improved gut health, especially during the highly-sensitive stage of infancy. Diet can affect the composition of the gut microflora through the availability of different substrates for bacterial fermentation. Differences in gut microflora composition and incidence of infection exist between breast-fed and formula-fed infants, with the former thought to have improved protection. Historically, this improvement has been believed to be a result of the higher presence of reportedly-beneficial genera such as the bifidobacteria. As such, functional food ingredients such as prebiotics and probiotics could effect a beneficial modification in the composition and activities of gut microflora of infants by increasing positive flora components. The prebiotic approach aims to increase resident bacteria that are considered to be beneficial for human health, e.g. bifidobacteria and lactobacilli, while probiotics advocates the use of the live micro-organisms themselves in the diet. Both approaches have found their way into infant formula feeds and aim to more closely simulate the gut microbiota composition seen during breast-feeding.

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a ‘hot spot’ for horizontal gene transfer between microbes.

Protective role of lactobacilli in Shigella dysenteriae 1–induced diarrhea in rats

OBJECTIVE

Studies on lactic acid bacteria exemplify their use against various enteropathogens in vitro. Nevertheless, in vivo effects of Lactobacillus during Shigella infection have not been evaluated. The present study evaluated the effect of Lactobacillus rhamnosus and Lactobacillus acidophilus on neutrophil infiltration and lipid peroxidation during Shigella dysenteriae 1-induced diarrhea in rats.

METHODS

The rats were divided into eight groups (n = 6 in each group). Induced rats received single oral dose of S. dysenteriae (12 x 10(8) colony-forming units [cfu]/mL). Treated rats received L. rhamnosus (1 x 10(7) cfu/mL) or L. acidophilus (1 x 10(7) cfu/mL) orally for 4 d, alone or in combination, followed by Shigella administration. At the end of the experimental period, animals were sacrificed and the assay of the activity of alkaline phosphatase, myeloperoxidase, and antioxidants and the estimation of lipid peroxides were performed. Activity staining of superoxide dismutase and catalase was done in addition to gelatin zymography for matrix metalloproteinase (MMP; MMP-2 and MMP-9) activity. A portion of the intestinal tissue was fixed in 10% formalin for histologic studies.

RESULTS

Administration of S. dysenteriae 1 alone resulted in increased levels of myeloperoxidase, lipid peroxidation, alkaline phosphatase, and the expression of MMP-2 and MMP-9 with concomitant decrease in the antioxidant levels. Pretreatment with the combination of L. rhamnosus (1 x 10(7) cfu/mL) and L. acidophilus (1 x 10(7) cfu/mL) significantly attenuated these changes when compared with the diseased group. Histologic observations were in correlation with biochemical parameters.

CONCLUSION

Lactobacillus rhamnosus plus L. acidophilus offered better protection when compared with individual treatment with these strains during Shigella infection.

Culture-independent analysis of bacterial diversity in a child-care facility

BACKGROUND

Child-care facilities appear to provide daily opportunities for exposure and transmission of bacteria and viruses. However, almost nothing is known about the diversity of microbial contamination in daycare facilities or its public health implications. Recent culture-independent molecular studies of bacterial diversity in indoor environments have revealed an astonishing diversity of microorganisms, including opportunistic pathogens and many uncultured bacteria. In this study, we used culture and culture-independent methods to determine the viability and diversity of bacteria in a child-care center over a six-month period.

RESULTS

We sampled surface contamination on toys and furniture using sterile cotton swabs in four daycare classrooms. Bacteria were isolated on nutrient and blood agar plates, and 16S rRNA gene sequences were obtained from unique (one of a kind) colony morphologies for species identification. We also extracted DNA directly from nine representative swab samples taken over the course of the study from both toy and furniture surfaces, and used "universal" 16S rRNA gene bacterial primers to create PCR-based clone libraries. The rRNA gene clones were sequenced, and the sequences were compared with related sequences in GenBank and subjected to phylogenetic analyses to determine their evolutionary relationships. Culturing methods identified viable bacteria on all toys and furniture surfaces sampled in the study. Bacillus spp. were the most commonly cultured bacteria, followed by Staphylococcus spp., and Microbacterium spp. Culture-independent methods based on 16S rRNA gene sequencing, on the other hand, revealed an entirely new dimension of microbial diversity, including an estimated 190 bacterial species from 15 bacterial divisions. Sequence comparisons and phylogenetic analyses determined that the clone libraries were dominated by a diverse set of sequences related to Pseudomonas spp., as well as uncultured bacteria originally identified on human vaginal epithelium. Other sequences were related to uncultured bacteria from wastewater sludge, and many human-associated bacteria including a number of pathogens and opportunistic pathogens. Our results suggest that the child-care facility provided an excellent habitat for slime-producing Pseudomonads, and that diaper changing contributed significantly to the bacterial contamination.

CONCLUSION

The combination of culture and culture-independent methods provided powerful means for determining both viability and diversity of bacteria in child-care facilities. Our results provided insight into the source of contamination and suggested ways in which sanitation might be improved. Although our study identified a remarkable array of microbial diversity present in a single daycare, it also revealed just how little we comprehend the true extent of microbial diversity in daycare centers or other indoor environments.