The normal microbial flora

A relational framework for microbiome research with Indigenous communities

Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely failed to include Indigenous people in knowledge co-production or benefit, perpetuating a legacy of intellectual and material extraction. We propose a framework centred on relationality among Indigenous peoples, researchers and microbes, to guide ethical microbiome research. Our framework centres accountability to flatten historical power imbalances that favour researcher perspectives and interests to provide space for Indigenous worldviews in pursuit of Indigenous research sovereignty. Ethical inclusion of Indigenous communities in microbiome research can provide health benefits for all populations and reinforce mutually beneficial partnerships between researchers and the public.

Restoration of the Original Inhabitants: A Systematic Review on Fecal Microbiota Transplantation for Graft-Versus-Host Disease

A compelling intervention to maintain healthy gut microbiota in graft-versus-host-disease (GVHD) is fecal microbial transplantation (FMT). To examine its role in GVHD, we conducted a systemic literature search using multiple electronic databases. Upon pooling of data, 79 patients from six studies and five case reports were included. Complete remission (CR) occurred in 55.9% of patients, and partial remission (PR) occurred in 26.5% of patients (82.4% overall response rate). A limited number of patients had treatment-related mortality (TRM), while few showed mild gastrointestinal (GI)-related and non-GI adverse effects. None of the studies directly examined the role of FMT in the prevention of GVHD. In conclusion, FMT seems to be a safe and effective strategy for the management of GVHD based on the current evidence. Due to the small number of patients evaluated and the absence of randomized data, one cannot portray FMT as a standard of care yet; however, the low toxicity along with the clinical improvement justifies this modality to be tested in a randomized fashion.

Microbial Diversity and Antibiotic Susceptibility Pattern of Bacteria Associated with Motorcycle Helmets

Background

Motorcycle helmets can serve as a potential vehicle for the transmission of pathogenic bacteria and fungi with serious health implications. The main aim of this study was to explore the microbial diversity associated with the motorcycle helmets and determine the antibiotic susceptibility profile of the bacterial isolates.

Methods

A descriptive cross-sectional study was carried out among the teaching staffs of Birendra Multiple Campus, Bharatpur, Nepal. A total of 130 motorcycle helmets worn by the teaching staffs of the Birendra Multiple Campus, Bharatpur, were included in the study for microbiological investigations.

Results

Of the total 130 motorcycle helmets analyzed, 392 bacteria and 346 fungi belonging to seven different genera were recovered. Staphylococcus aureus 89 (22.7%) was the predominant bacteria followed by S. epidermidis 77 (19.6%) and E. coli 54 (13.8%), whereas Aspergillus niger 67 (19.4%) was the predominant fungi followed by A. fumigatus 49 (14.2%). Antibiotic susceptibility test was performed by the disc diffusion method for all the bacterial isolates. Tetracycline, gentamycin, and cotrimoxazole were the most effective antibiotics for Gram-positive isolates, whereas Gram-negative isolates were sensitive towards imipenem and ciprofloxacin. Of the total bacterial isolates, 153 (39.0%) were multidrug-resistant (MDR), 10.4% were extended-spectrum beta-lactamase (ESBL) producers, and 4.3% were metallo-beta-lactamase (MBL) producers and, out of 89 isolates of Staphylococcus aureus, 30 (33.7%) were detected as methicillin-resistant Staphylococcus aureus (MRSA).

Conclusion

The findings suggest that motorcycle riders should follow good hygiene practices and regularly clean their helmets with suitable sterilants to avoid the risk of microbial contamination and reduce the associated risks.

A New Benchmark to Determine What Healthy Western Skin Looks Like in Terms of Biodiversity Using Standardised Methodology

A significant loss of microbial biodiversity on the skin has been linked to an increased prevalence of skin problems in the western world. The primary objective of this study was to obtain a benchmark value for the microbial diversity found on healthy western skin, using the Chao1 index. This benchmark was used to update our 2017 skin health measuring mechanism in line with standardised methodology. It used 50 human participants from Graz in Austria and at a read depth of 6600 sequences, we found the average Chao1 diversity to be ~180, with upper and lower quartiles of ~208 and ~150, respectively. Previous work with a larger sample size was unsatisfactory to use as a benchmark because different diversity indices and evaluation methodologies were used. The Medical University of Graz used the most recent version of the Chao1 index to obtain diversity results. Because of this study, we can transfer other benchmarks of skin microbiome diversity to the methodology used in this work from our 2017 study, such as “unhealthy western skin” and “caveman/perfect skin”. This could aid with the diagnostic assessment of susceptibility to cutaneous conditions or diseases and treatment. We also investigated the effect of sex and age, which are two known skin microbiome affecting factors. Although no statistical significance is seen for sex- and age-related changes in diversity, there appear to be changes related to both. Our preliminary results (10 in each of the five age groups) show adults aged 28–37 have the highest average diversity, and adults aged 48–57 have the lowest average diversity. In future work, this could be improved by obtaining benchmark diversity values from a larger sample size for any age, sex, body site, and area of residence, to which subjects can be compared. These improvements could help to investigate the ultimate question regarding which environmental factors in the western world are the main cause of the huge rise in skin problems. This could lead to future restrictions of certain synthetic chemicals or products found to be particularly harmful to the skin.

Skin microbiome differences relate to the grade of acne vulgaris

The skin microbiome plays important roles in the pathogenesis and development of acne. We aimed to investigate the facial skin microbiome of acne and microbiome differences related to different grades of acne. Skin swabs from nine healthy controls and 67 acne patients were collected, and the skin microbiomes were analyzed using 16S rRNA gene sequencing. Compared with healthy controls, acne patients harbored significantly altered skin microbiomes. The skin microbiomes of patients with grade 1-3 acne were similar, but patients with grade 4 acne showed a significantly different skin microbiome compared with grade 1-3 acne, including increased alpha diversity and increased proportions of four Gram-negative bacteria (Faecalibacterium, Klebsiella, Odoribacter and Bacteroides). In conclusion, acne patients harbored an altered skin microbiome, and more significant dysbiosis was found in patients with grade 4 acne (severe acne). Our findings may provide evidence for the pathogenic mechanisms of acne and microbial-based strategies to avoid and treat acne, especially grade 4 acne.

The Role of Every-Day Cosmetics in Altering the Skin Microbiome: A Study Using Biodiversity

As described in previous work, the use of synthetic chemical ingredients in modern cosmetics is postulated to be a cause of damage to the skin microbiome. The discovery that biodiversity on the human skin is currently the only reliable indicator of skin health, meant that for the first time, a mechanism to test for healthy skin was possible. Using this mechanism and in collaboration with The Medical University of Graz, who carried out the independent study, this work aimed to help answer whether modern day synthetic cosmetics are a main cause of long-term damage to the skin microbiome. Thirty-two human participants tested three different face washes for their effect on the skin’s microbial diversity, along with skin pH, moisture and TEWL (trans-epidermal water loss), washing twice-a-day for four weeks. The upper volar forearm of the volunteers was swabbed at the beginning, two weeks in and at the end of the four weeks. 16S rRNA sequencing was used. One leading ‘natural’ brand full of synthetic ingredients, a leading synthetic brand and a 100% natural face wash were used. Results give the first indications of a link between synthetic ingredients in a cosmetics product and its effect on skin microbiome biodiversity. It paves the way for future studies on the topic with a larger sample group, longer test period and standardised methodology to create a universal standard for testing the health of skin using benchmark diversity values. This can be used in the future to test the effectiveness of cosmetics or ingredients on skin health, leading to the restriction in cosmetics of products proven to harm the skin’s natural environment.

Oropharyngeal colonization: epidemiology, treatment and ventilator-associated pneumonia prevention

Oropharyngeal (OP) colonization and ventilator-associated pneumonia (VAP) mechanisms are tightly linked. A significant within-population variation in OP colonization has been described, with its composition being dependent from patients' severity. For instance, healthy subjects have a very low rate in Gram-negative bacteria (GNB) colonization, while its rate rises in comorbid patients, reaching high proportions in ICU patients. Various factors can be put forward to explain the modifications of hospital acquired OP. ICU patients might suffer from underlying diseases; the gastric reflux induced by the presence of nasogastric tubes and the patients' position influences OP colonization; salivary composition might influence OP content, as it modulates bacterial adhesion and induces reversible bacterial changes enhancing bacterial binding. The transition from OP colonization to VAP has been shown in numerous studies, with the digestive tract acting as a filter, or as a reservoir. Some therapies have been investigated to modulate OP colonization, in order to reduce the risk for VAP. Among those, mammalian antimicrobial peptides have been shown effective in reducing GNB colonization in healthy subjects, but failed in preventing VAP in ICU patients. The widely used chlorhexidine was tested in numerous trials. Data on its efficacy are conflicting, and meta-analyses yield discordant results. Above all, several drawbacks have aroused: a poor tolerance of concentrated solutions; an increased risk of death in the less severe patients; and a reduced susceptibility towards chlorhexidine of number of VAP pathogens. Proanthocyanidins, used to prevent Escherichia coli adhesion to the urothelium, have been tested in mice model of pneumonia with interesting results. Some complementary data are needed before moving to clinical research. Future research paths should include a reappraisal of OP colonization; finding better formulations for chlorhexidine; define the best populations to target oral decontamination and developing other strategies to prevent and treat OP colonization.

The dorsal skin structure contributes to the surface bacteria populations of Sunda Porcupine (Hystrix javanica)

Skin becomes the largest organ in the body and protects its own inner layer. The structure and chemical composition of the skin contribute to skin condition and affect the habitat of certain bacteria. The Sunda Porcupine is one of endemic animals of Indonesia which possesses quill as the main derivate of its skin and as a defence tool against predators. The present study used nine adults (five females and four males) of Sunda Porcupine and aimed to observe the correlation of skin structure with bacterial population at the surface level. The skin was wavy due to the protrusion of quill follicle orifices on the skin surface and formed clusters. The skin of Sunda Porcupine was also wrinkled and had a lot of flakiness. Histologically, the skin was composed of epidermis, dermis, hypodermis and subcutaneous muscle. The quill follicles and their properties were the dominant structure component of the skin. No sweat gland was observed in the skin of the Sunda Porcupine, and sebaceous gland was found only around quill and hair follicles. The bacterias identified in the skin were Staphylococcus aureus, S. epidermidis, Micrococcus sp. and Salmonella sp. When compared, the bacterial population was higher in the lumbosacral region than in the thoracodorsal region, but the difference was not significant. The density of quill clusters was negatively correlated to the bacterial population. It was suggested the structure of the skin has contribution to bacterial population in dorsal trunk of the Sunda Porcupine.

Conjunctival Microbial Flora in Ocular Stevens-Johnson Syndrome Sequelae Patients at a Tertiary Eye Care Center

PURPOSE

To evaluate the conjunctival microbial flora in cases of ocular Stevens-Johnson Syndrome (SJS) in a tertiary eye care center.

METHODS

This prospective study comprised 176 eyes of 88 patients with ocular SJS compared with 124 eyes of normal subjects. The conjunctival swabs were collected and sent for microbiological analysis for bacterial isolation and antibiotic sensitivity examination. The type of bacteria isolated and its antibiotic sensitivity pattern were studied.

RESULTS

Of 176 eyes, 104 (59%) had positive cultures for bacteria in cases of SJS and 16 (12.9%) had positive culture in the control group, the difference being statistically significant (P = 0.001). In the SJS group, 14 different types of bacterial isolates were identified. The most common isolate was coagulase-negative staphylococci (CNS) (30/104, 28.8%) followed by Corynebacteria species (35/104, 33.6%) and Staphylococcus aureus (19/104, 18.2%). More than 1 bacteria were isolated in 7 eyes (6.7%). Most of the isolates showed resistance to ciprofloxacin with no resistance to gatifloxacin and moxifloxacin. In the control group, only 2 bacteria were isolated, which included CNS (14/16, 87.5%) and Streptococcus pneumoniae (2/16, 12.5%). CNS showed resistance to ciprofloxacin, and S. pneumoniae was resistant to tobramycin and gentamycin.

CONCLUSIONS

Ocular SJS is associated with alteration of the normal microbial flora residing in the conjunctival sac. The study of which is vital in cases of infection in these eyes with compromised ocular surface. Mixed flora are seen more often in cases of ocular SJS as compared with controls.

Factors shaping the composition of the cutaneous microbiota

From birth, we are constantly exposed to bacteria, fungi and viruses, some of which are capable of transiently or permanently inhabiting our different body parts as our microbiota. The majority of our microbial interactions occur during and after birth, and several different factors, including age, sex, genetic constitution, environmental conditions and lifestyle, have been suggested to shape the composition of this microbial community. Propionibacterium acnes is one of the most dominant lipophilic microbes of the postadolescent, sebum-rich human skin regions. Currently, the role of this bacterium in the pathogenesis of the most common inflammatory skin disease, acne vulgaris, is a topic of intense scientific debate. Recent results suggest that Westernization strongly increases the dominance of the Propionibacterium genus in human skin compared with natural populations living more traditional lifestyles. According to the disappearing microbiota hypothesis proposed by Martin Blaser, such alterations in the composition of our microbiota are the possible consequences of socioeconomic and lifestyle changes occurring after the industrial revolution. Evanescence of species that are important elements of the human ecosystem might lead to the overgrowth and subsequent dominance of others because of the lack of ecological competition. Such changes can disturb the fine-tuned balance of the human body and, accordingly, our microbes developed through a long co-evolutionary process. These processes might lead to the transformation of a seemingly harmless species into an opportunistic pathogen through bacterial dysbiosis. This might have happened in the case of P. acnes in acne pathogenesis.

Efficacy of Trans-cinnamaldehyde and Eugenol in Reducing Acinetobacter baumannii Adhesion to and Invasion of Human Keratinocytes and Controlling Wound Infection In Vitro

The study investigated the efficacy of two natural, plant-derived antimicrobials (PDAs), namely trans-cinnamaldehyde (TC), and eugenol (EG) for decreasing Acinetobacter baumannii adhesion to and invasion of human keratinocytes (HEK001). Moreover, the efficacy of two PDAs for inhibiting A. baumannii biofilm formation was determined using an in vitro collagen matrix wound model. Additionally, the effect of TC and EG on A. baumannii biofilm architecture was visualized using confocal scanning microscopy. Further the effect of both PDAs on genes critical for biofilm synthesis was determined using real-time quantitative polymerase chain reaction. Both TC and EG significantly reduced A. baumannii adhesion and invasion to HEK001 by ~2 to 3 log₁₀ CFU/mL (p < 0.05) compared with the controls (p < 0.05). Further, after 24 and 48 h, TC and EG inhibited biofilm formation by ~1.5 to 2 and ~2 to 3.5 log₁₀ CFU/mL, compared with controls (p < 0.05). Confocal microscopy revealed that TC and EG disrupted the biofilm architecture. RT-qPCR results indicated that two phytochemicals significantly down-regulated the transcription of genes associated with A. baumannii biofilm production. The results suggest that both TC and EG could potentially be used to treat A. baumannii wound infections; however, their efficacy in in vivo models needs to be validated. Copyright © 2016 John Wiley & Sons, Ltd.

Dynamics of Nasopharyngitis in Children

PURPOSE: Our goal was to characterize the dynamics and bacterial interaction of the aerobic and anaerobic flora of nasal discharge of children at different stages of uncomplicated nasopharyngitis.

METHODS AND PATIENTS: Serial semiquantitative nasopharyngeal (NP) and quantitative nasal discharge (ND) cultures were taken every 3 to 5 days from 20 children in whom purulent discharge eventually developed (group 1), and a single culture was obtained from a group of 20 who had only clear discharge (group 2).

RESULTS: Aerobic and anaerobic bacteria were isolated from all NP cultures. Bacterial growth was present in 8 (40%) NDs of group 2. Only 7 (35%) of the clear NDs of group 1 showed bacterial growth; the number increased to 14 (70%) at the mucoid stage and 20 (100%) at the purulent stage. It declined to 6 (30%) at the final clear stage. The number of species and total number of organisms increased in the NDs of group 1. Group 1 patients had higher recovery rates of Streptococcus pneumoniae and Haemophilus influenzae in their NP cultures than group 2 patients (P > 0.05). During the purulent stage, Peptostreptococcus species were isolated in 15 (75%), Fusobacterium species in 10 (50%), Prevotella species in 9 (45%), H influenzae in 8 (40%), S pneumoniae in 6 (30%), and β-hemolytic streptococci in 5 (25%) of group 1 NDs. This was higher than their recovery in the clear stages of both groups and the mucoid stage of group 1. A total of 8 organisms capable of interfering with the growth of potential pathogens were isolated from the NPs of group 1, as compared with 35 from group 2 ( P > 0.001).

CONCLUSIONS: The development of purulent nasopharyngitis is associated with the pre-existing presence of potential pathogens and the absence of interfering organisms.

Influence and effect of the human microbiome in allergy and asthma

PURPOSE OF REVIEW

Studies have illustrated that the healthy human microbiome (i.e. the communities of microbes, their genomic content and interaction with the host) plays a role in the maintenance of immune homeostasis. Perturbation of these communities is an emerging characteristic of an increasing number of inflammatory diseases. The goal of this article is to review the current literature on both respiratory and gut microbiomes and their established relationship with allergy and asthma.

RECENT FINDINGS

Multiple studies have demonstrated airway microbiota dysbiosis, characterized by Proteobacteria expansion in the lower airways, to be a consistent trait of established adult asthma. Members of this phylum are associated with disease features such as bronchial hyperreactivity or corticosteroid resistance. Emerging evidence implicates the neonatal gut microbiome as playing a significant role in the development of childhood atopy, a common precursor to asthma. Murine studies have demonstrated that specific bacterial species (e.g. Lactobacillus johnsonii, Bacteroides fragilis) and microbial metabolites (e.g. the short-chain fatty acid propionate), when supplemented to animals, confer protection against allergen-induced airway disorders.

SUMMARY

The emerging view of atopy and asthma is one consistently related to inappropriate microbial community composition and function in both the airway and gastrointestinal tract. This opens up the possibility that strategies to rationally manipulate microbiota at these sites may represent a novel approach to disease prevention or management.

The human microbiota: the rise of an "empire"

The human body hosts rich and diverse microbial communities. Our microbiota affects the normal human physiology, and compositional changes might alter host homeostasis and, therefore, disease risk. The microbial community structure may sometimes occupy discrete configurations and under certain circumstances vary continuously. The ability to characterize accurately the ecology of human-associated microbial communities became possible by advances in deep sequencing and bioinformatics analyses.

Host demise as a beneficial function of indigenous microbiota in human hosts

The age structure of human populations is exceptional among animal species. Unlike with most species, human juvenility is extremely extended, and death is not coincident with the end of the reproductive period. We examine the age structure of early humans with models that reveal an extraordinary balance of human fertility and mortality. We hypothesize that the age structure of early humans was maintained by mechanisms incorporating the programmed death of senescent individuals, including by means of interactions with their indigenous microorganisms. First, before and during reproductive life, there was selection for microbes that preserve host function through regulation of energy homeostasis, promotion of fecundity, and defense against competing high-grade pathogens. Second, we hypothesize that after reproductive life, there was selection for organisms that contribute to host demise. While deleterious to the individual, the presence of such interplay may be salutary for the overall host population in terms of resource utilization, resistance to periodic diminutions in the food supply, and epidemics due to high-grade pathogens. We provide deterministic mathematical models based on age-structured populations that illustrate the dynamics of such relationships and explore the relevant parameter values within which population viability is maintained. We argue that the age structure of early humans was robust in its balance of the juvenile, reproductive-age, and senescent classes. These concepts are relevant to issues in modern human longevity, including inflammation-induced neoplasia and degenerative diseases of the elderly, which are a legacy of human evolution.

IMPORTANCE

The extended longevity of modern humans is a very recent societal artifact, although it is inherent in human evolution. The age structure of early humans was balanced by fertility and mortality, with an exceptionally prolonged juvenility. We examined the role of indigenous microbes in early humans as fundamental contributors to this age structure. We hypothesize that the human microbiome evolved mechanisms specific to the mortality of senescent individuals among early humans because their mortality contributed to the stability of the general population. The hypothesis that we present provides new bases for modern medical problems, such as inflammation-induced neoplasia and degenerative diseases of the elderly. We postulate that these mechanisms evolved because they contributed to the stability of early human populations, but their legacy is now a burden on human longevity in the changed modern world.

The microbiome revolution

The collection of bacteria, viruses, and fungi that live in and on the human body, collectively known as the microbiome, has recently emerged as an important factor in human physiology and disease. The gut in particular is a biological niche that is home to a diverse array of microbes that influence nearly all aspects of human biology through their interactions with their host; new technologies are beginning to reveal important aspects of host-microbe interactions. Articles in this Review series address how perturbations of the microbiota, such as through antibiotic use, influence its overall structure and function; how our microbiome influences the impact of infectious agents, such as C. difficile; how our microbiome mediates metabolism of xenobiotics; how the microbiota contribute to immunity as well as to metabolic and inflammatory diseases; and the role of commensal microbes in oncogenesis.

Aspiration pneumonia: a review of modern trends

PURPOSE

The purpose was to describe aspiration pneumonia in the context of other lung infections and aspiration syndromes and to distinguish between the main scenarios commonly implied when the terms aspiration or aspiration pneumonia are used. Finally, we aim to summarize current evidence surrounding the diagnosis, microbiology, treatment, risks, and prevention of aspiration pneumonia.

MATERIALS AND METHODS

Medline was searched from inception to November 2013. All descriptive or experimental studies that added to the understanding of aspiration pneumonia were reviewed. All studies that provided insight into the clinical aspiration syndromes, historical context, diagnosis, microbiology, risk factors, prevention, and treatment were summarized within the text.

RESULTS

Despite the original teaching, aspiration pneumonia is difficult to distinguish from other pneumonia syndromes. The microbiology of pneumonia after a macroaspiration has changed over the last 60 years from an anaerobic infection to one of aerobic and nosocomial bacteria. Successful antibiotic therapy has been achieved with several antibiotics. Various risks for aspiration have been described leading to several proposed preventative measures.

CONCLUSIONS

Aspiration pneumonia is a disease with a distinct pathophysiology. In the modern era, aspiration pneumonia is rarely solely an anaerobic infection. Antibiotic treatment is largely dependent on the clinical scenario. Several measures may help prevent aspiration pneumonia.

Rhinovirus infections and adenoidal hypertrophy: do they interact with atopy in children?

Modern diagnostic methods allow the evaluation of the connection between rhinoviruses and atopy. Recent studies suggest that rhinoviruses are present in the adenoids at higher titers than in other specific sites, after inoculation of nasal mucosa or conjunctiva in volunteers. Therefore, it is possible that they might be responsible for specific local changes, while such changes may be influenced by atopy. This review focuses on the interactions between rhinoviral infection, the host's immune status and adenoidal disease.

Exploring bacterial flora in oral squamous cell carcinoma: a microbiological study

The oral cavity contains a unique and diverse microflora. While most of these organisms exhibit commensalism, shifts in bacterial community dynamics cause pathological changes within the oral cavity and at distant sites. We assessed the microbial flora using cultured saliva and oral swabs from subjects with oral squamous cell carcinoma (OSCC) and healthy controls. Microbial samples were collected from the carcinoma site, contralateral healthy mucosa, and saliva of the study group and samples were collected from healthy mucosa and saliva of controls. Samples were stored on ice and transported to the laboratory for culture. The median number of colony forming units (CFU)/ml at carcinoma sites was significantly greater than at the contralateral healthy mucosa. Similarly, in saliva of carcinoma subjects, the median number of CFU/ml was significantly greater than in saliva of control subjects.

Colonization of the mouse upper gastrointestinal tract by lactobacillus murinus: a histological, immunocytochemical, and ultrastructural study

Lactobacillus is normally present in animals and humans colonizing several epithelia, mainly those belonging to the upper gastrointestinal tract. Most of the information about the distribution of Lactobacillus in mice has been obtained by bacterial culture and characterization, and only few reports have described the direct presence of these bacteria in tissues, especially in the gastric mucosa. In this study, we have characterized and evaluated the location and detailed relationship between Lactobacillus and epithelia using a combination of histological, molecular, immunocytochemical and ultrastructural methods. Normal Balb/c mice were sacrificed to study esophagus and stomach. Partial 16S rRNA gene sequencing, Gram, and P.A. Schiff staining allowed us to demonstrate that Lactobacillus murinus isolated from each animal colonize not only the epithelium of the forestomach but also that belonging to the distal esophagus. The pattern of colonization was linear over the keratinized epithelium, and also in a vertical way of focal bacterial aggregates. This was confirmed by transmission electron microscopy, and the nature of bacteria was further assessed by immunocytochemistry. Our results indicate that L. murinus can colonize the stomach and the esophagus epithelia in a biofilm-like manner, possibly acting as a defense barrier against colonization by other bacteria.

Novel developmental analyses identify longitudinal patterns of early gut microbiota that affect infant growth

It is acknowledged that some obesity trajectories are set early in life, and that rapid weight gain in infancy is a risk factor for later development of obesity. Identifying modifiable factors associated with early rapid weight gain is a prerequisite for curtailing the growing worldwide obesity epidemic. Recently, much attention has been given to findings indicating that gut microbiota may play a role in obesity development. We aim at identifying how the development of early gut microbiota is associated with expected infant growth. We developed a novel procedure that allows for the identification of longitudinal gut microbiota patterns (corresponding to the gut ecosystem developing), which are associated with an outcome of interest, while appropriately controlling for the false discovery rate. Our method identified developmental pathways of Staphylococcus species and Escherichia coli that were associated with expected growth, and traditional methods indicated that the detection of Bacteroides species at day 30 was associated with growth. Our method should have wide future applicability for studying gut microbiota, and is particularly important for translational considerations, as it is critical to understand the timing of microbiome transitions prior to attempting to manipulate gut microbiota in early life.

Some obesity trajectories are set early in life, with rapid weight gain being a risk factor for later development of obesity. Recently, much attention has been given to findings indicating that gut microbiota may play a role in obesity development. The existence of time-dependent exposure windows, which rely on stimuli from the gut to initiate healthy development, gives the evolution of early life gut microbiota a critical role in human health. We identified children that followed their expected growth trajectories at six months of life, and those that had deviated. We then developed a novel statistical approach that allowed the identification of longitudinal gut microbiota patterns (e.g. a particular species was detected at days 4, 10, and 30 and not detected at day 120) that were associated with expected growth, while appropriately restricting the false discovery rate. We further identified when a deviation from the proposed longitudinal gut microbiota patterns would result in an abnormal growth outcome (either rapid or decreased growth at six months of life). We found developmental pathways of Staphylococcus species and Escherichia coli that were associated with expected growth, as well as indications that Bacteroides species at day 30 was associated with growth.

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.

Demonstration of substances of innate immunity in the esophageal epithelium of domesticated mammals. Part I--Methods and evaluation of comparative fixation

The aim of the investigation was to demonstrate that the esophageal epithelium of domesticated mammals exhibits characteristic features of innate immunity. The esophageal samples used were obtained immediately after euthanization from seven species of domesticated mammals of three nutrition groups (herbivores: horse, goat, cattle; omnivores: pig, dog, laboratory rat; carnivores: cat). The experimental basis was immunohistochemistry, which was evaluated in a qualitative and statistically relevant semi-quantitative manner. The first part of the study analyzed the influence of different fixation media on the immunohistochemical reactivities. Two formalin-based routine fixation solutions (Bouin's solution, Ca-acetate formalin) were compared with the recently introduced formalin-free HOPE® fixative. In this context, we clearly demonstrated a diminished immunoreactivity for Ca-formol fixed samples; satisfactory results were obtained, particularly, from samples fixed in Bouin's solution. The HOPE® fixation method offers a relatively cheap alternative, as the antibody amounts can be reduced. An application in routine diagnostic is not advisable, because of several variable parameters. It can be concluded that immunohistochemical results have always to be evaluated and discussed in close relation to the fixation medium used.

Irrigation of continent catheterizable ileal pouches: tap water can replace sterile solutions because it is safe, easy, and economical

BACKGROUND

Continent catheterizable ileal pouches require regular irrigations to reduce the risk of bacteriuria and urinary tract infections (UTIs).

OBJECTIVE

Our aim was to compare the UTI rate, patient friendliness, and costs of standard sterile irrigation versus irrigation with tap water.

DESIGN, SETTING, AND PARTICIPANTS

Twenty-three patients participated in a prospective randomized two-arm crossover single-center trial. Aseptic intermittent self-catheterization (ISC) combined with sterile sodium chloride (NaCl) 0.9% irrigation was compared with clean ISC and irrigation with tap water (H(2)O) during two study periods of 90 d each.

INTERVENTION

Patients underwent daily pouch irrigations with NaCl 0.9% solution or tap water.

MEASUREMENTS

Urine nitrite dipstick tests were evaluated daily; urine culture (UC) and patient friendliness were evaluated monthly. Costs were documented.

RESULTS AND LIMITATIONS

A total of 3916 study days with nitrite testing and irrigation were analyzed, 1876 (48%) in the NaCl arm and 2040 (52%) in the H(2)O arm. In the NaCl arm, 418 study days (22%) with nitrite-positive dipsticks were recorded, 219 d (11%) in the H(2)O arm, significantly fewer (p=0.01). Of the 149 UCs, 96 (64%) were positive, 48 in each arm, revealing a total of 16 different germs. All patients preferred the H(2)O method. Monthly costs were up to 20 times lower in the H(2)O arm.

CONCLUSIONS

Pouch irrigation with sterile NaCl 0.9% solution and tap water had comparable rates of positive UC. Irrigation with tap water significantly lowered the incidence of nitrite-positive study days and was substantially less costly and more patient friendly than NaCl irrigation. We therefore recommend the use of tap water (or bottled water) instead of sterile NaCl 0.9% solution for daily irrigation of continent catheterizable ileal pouches.

TRIAL REGISTRATION

Australian New Zealand Clinical Trials Registry, ACTRN12610000618055, http://www.ANZCTR.org.au/ACTRN12610000618055.aspx.

Staphylococcus epidermidis Esp inhibits Staphylococcus aureus biofilm formation and nasal colonization

Commensal bacteria are known to inhibit pathogen colonization; however, complex host-microbe and microbe-microbe interactions have made it difficult to gain a detailed understanding of the mechanisms involved in the inhibition of colonization. Here we show that the serine protease Esp secreted by a subset of Staphylococcus epidermidis, a commensal bacterium, inhibits biofilm formation and nasal colonization by Staphylococcus aureus, a human pathogen. Epidemiological studies have demonstrated that the presence of Esp-secreting S. epidermidis in the nasal cavities of human volunteers correlates with the absence of S. aureus. Purified Esp inhibits biofilm formation and destroys pre-existing S. aureus biofilms. Furthermore, Esp enhances the susceptibility of S. aureus in biofilms to immune system components. In vivo studies have shown that Esp-secreting S. epidermidis eliminates S. aureus nasal colonization. These findings indicate that Esp hinders S. aureus colonization in vivo through a novel mechanism of bacterial interference, which could lead to the development of novel therapeutics to prevent S. aureus colonization and infection.

The microbiome and obesity: is obesity linked to our gut flora?

The human gut is a lush microbial ecosystem containing about 100 trillion microorganisms, whose collective genome, the microbiome, contains 100-fold more genes than the entire human genome. The symbiosis of our extended genome plays a role in host homeostasis and energy extraction from diet. In this article, we summarize some of the studies that have advanced the understanding of the microbiome and its effects on metabolism, obesity, and health. Metagenomic studies demonstrated that certain mixes of gut microbiota may protect or predispose the host to obesity. Furthermore, microbiota transplantation studies in germ-free murine models showed that the efficient energy extraction traits of obese-type gut flora are transmissible. The proposed methods by which the microbiome may contribute to obesity include increasing dietary energy harvest, promoting fat deposition, and triggering systemic inflammation. Future treatments for obesity may involve modulation of gut microbiota using probiotics or prebiotics.

Do you have a probiotic in your future?

The possibility of using microbes to maintain health, and to prevent or treat disease is a topic as old as microbiology. However, one factor impeding the introduction of effective probiotics has been our very limited understanding of the composition of the human microbiome, as well as the biological requirements for these organisms. With advances in understanding the microbiome and its metagenome in humans and other mammals, we now can build a more robust scientific basis to develop probiotic strategies. Increasing knowledge of intramicrobial competition and cooperation, as well as host-microbe cross-signaling, will facilitate design of new probiotics and the modeling of their deployment, leading to eventual clinical trials.

Characterization of mucosal biofilms on human adenoid tissues

OBJECTIVES

To demonstrate the presence of mucosal biofilm in adenoid tissue using double staining for visualization of both the bacterial matrix and the bacterial cells. To identify bacterial species present on the surface of the studied adenoids.

STUDY DESIGN

Prospective study.

METHODS

A total of 39 specimens of adenoidectomy were removed from children with chronic and/or recurrent otitis media. The specimens were prepared for light microscopy using Gram staining, scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Double staining was performed with CLSM to visualize both the bacteria and the glycocalyx matrix. Nine adenoids on which bacterial biofilms were visualized with CLSM were used for identification of bacterial species by 16S-DNA polymerase chain reaction (PCR) amplification and homology analysis.

RESULTS

Of the 39 adenoids investigated, 22 (54%) showed evidence of mucosal biofilms. Gram staining, SEM and CLSM showed the presence of bacterial cells, organized in bacterial microcolonies. CLSM with double staining demonstrated mucosal biofilms by showing the presence of both bacteria and the glycocalyx. The use of 16S-DNA polymerase chain reaction (PCR) amplification and subsequent sequence analyses identified the presence of Corynebacterium argentoratense, Streptococcus salivarius, Micrococcus luteus, and Staphylococcus aureus.

CONCLUSIONS

This study demonstrates that adenoid tissue in children with chronic or/and recurrent otitis media contains mucosal biofilms in 54% of the cases. The existence of living bacteria has been demonstrated. Further studies are required to describe the panel of bacteria that can be harbored in the biofilms present in adenoids and the mechanisms involved in the physiopathology of otitis prone children.

[Intestinal microbiota of individuals who suffered occupational accidents with biological materials and underwent antiretroviral prophylaxis]

The aim of this study was to evaluate the intestinal microbiota of individuals who had suffered occupational accidents and had received antiretrovirals. The study group consisted of 23 individuals between 18 and 45 years old, of whom 13 were blood donors and 10 had suffered occupational accidents. Intestinal microflora, anthropometry and laboratory tests were evaluated before, after and 30 days after discontinuation of the medication. Zidovudine plus lamivudine was used in association with nelfinavir for 70% of the individuals, with efavirenz for 20% and with ritonavir for 10%. Nutritional, diet, laboratory and intestinal microbiota abnormalities were analyzed at three times: M1, not more than two days after starting prophylaxis; M2, on the last day of prophylaxis; and M3, 30 days after ending prophylaxis. Nausea, vomiting and diarrhea were present in 50% at M2. Overweight in 70%, malnutrition and eutrophy in 10% of the individuals remained unchanged during the study. Transaminases, triglycerides and LDL-cholesterol because elevated at M2 and normalized 30 days after discontinuation of the medication. There were significant reductions in Lactobacillus, Bifidobacterium and Bacteroides at the three times. The use of antiretrovirals caused a significant impact on the individuals intestinal microbiota, without recovery after 30 days.

Bacterial Infections

In Osier’s time, bacterial pneumonia was a dreaded event, so important that he borrowed John Bunyan’s characterization of tuberculosis and anointed the pneumococcus, as the prime pathogen, “Captain of the men of death.”1 One hundred years later much has changed, but much remains the same. Pneumonia is now the sixth most common cause of death and the most common lethal infection in the United States. Hospital-acquired pneumonia is now the second most common nosocomial infection.2 It was documented as a complication in 0.6% of patients in a national surveillance study,3 and has been reported in as many as 20% of patients in critical care units.4 Furthermore, it is the leading cause of death among nosocomial infections.5 Leu and colleagues6 were able to associate one third of the mortality in patients with nosocomial pneumonia to the infection itself. The increase in hospital stay, which averaged 7 days, was statistically significant. It has been estimated that nosocomial pneumonia produces costs in excess of $500 million each year in the United States, largely related to the increased length of hospital stay.