The human microbiota: the rise of an "empire"

Impaired oral health: a required companion of bacterial aspiration pneumonia

Laryngotracheal aspiration has a widely-held reputation as a primary cause of lower respiratory infections, such as pneumonia, and is a major concern of care providers of the seriously ill orelderly frail patient. Laryngeal mechanical inefficiency resulting in aspiration into the lower respiratory tract, by itself, is not the cause of pneumonia. It is but one of several factors that must be present simultaneously for pneumonia to develop. Aspiration of oral and gastric contentsoccurs often in healthy people of all ages and without significant pulmonary consequences. Inthe seriously ill or elderly frail patient, higher concentrations of pathogens in the contents of theaspirate are the primary catalyst for pulmonary infection development if in an immunocompromised lower respiratory system. The oral cavity is a complex and ever changing eco-environment striving to maintain homogeneity among the numerous microbial communities inhabiting its surfaces. Poor maintenance of these surfaces to prevent infection can result inpathogenic changes to these microbial communities and, with subsequent proliferation, can altermicrobial communities in the tracheal and bronchial passages. Higher bacterial pathogen concentrations mixing with oral secretions, or with foods, when aspirated into an immunecompromised lower respiratory complex, may result in bacterial aspiration pneumonia development, or other respiratory or systemic diseases. A large volume of clinical evidence makes it clear that oral cleaning regimens, when used in caring for ill or frail patients in hospitals and long-term care facilities, drastically reduce the incidence of respiratory infection and death. The purpose of this narrative review is to examine oral health as a required causative companionin bacterial aspiration pneumonia development, and the effectiveness of oral infection control inthe prevention of this disease.

Bacteria in the oral cavity of individuals consuming intoxicating substances

Food habits and oral hygiene are critical attributes for physiochemical environment of the oral cavity. Consumption of intoxicating substances such as betel nut ('Tamul'), alcohol, smoking and chewing tobacco may strongly influence the oral ecosystem including commensal microbes. Therefore, a comparative assessment of microbes in the oral cavity between individuals consuming intoxicating substances and non-consumers may indicate the influence of these substances. Oral swabs were collected from consumers of intoxicating substances and non- consumers of Assam, India, microbes were isolated by culturing on Nutrient agar and identified by phylogenetic analysis of their 16S rRNA gene sequences. The risks of consumption of intoxicating substance on occurrence of microbes and health conditions were estimated using binary logistic regression. Mostly pathogens and opportunistic pathogens were found in the oral cavity of consumers and oral cancer patients which included Pseudomonas aeruginosa, Serratia marcescens, Rhodococcus antrifimi, Paenibacillus dendritiformis, Bacillus cereus, Staphylococcus carnosus, Klebsiella michiganensis and Pseudomonas cedrina. Enterobacter hormaechei was found in the oral cavity of cancer patients but not in other cases. Pseudomonas sp. were found to be widely distributed. The risk of occurrence of these organisms were found in between 0.01 and 2.963 odds and health conditions between 0.088 and 10.148 odds on exposure to different intoxicating substances. When exposed to microbes, the risk of varying health conditions ranged between 0.108 and 2.306 odds. Chewing tobacco showed a higher risk for oral cancer (10.148 odds). Prolonged exposure to intoxicating substances conduce a favorable environment for the pathogens and opportunistic pathogens to colonize in the oral cavity of individuals consuming intoxicating substances.

Impact of Oral Microbiome in Periodontal Health and Periodontitis: A Critical Review on Prevention and Treatment

The skin, oral cavity, digestive and reproductive tracts of the human body harbor symbiotic and commensal microorganisms living harmoniously with the host. The oral cavity houses one of the most heterogeneous microbial communities found in the human organism, ranking second in terms of species diversity and complexity only to the gastrointestinal microbiota and including bacteria, archaea, fungi, and viruses. The accumulation of microbial plaque in the oral cavity may lead, in susceptible individuals, to a complex host-mediated inflammatory and immune response representing the primary etiological factor of periodontal damage that occurs in periodontitis. Periodontal disease is a chronic inflammatory condition affecting about 20-50% of people worldwide and manifesting clinically through the detection of gingival inflammation, clinical attachment loss (CAL), radiographic assessed resorption of alveolar bone, periodontal pockets, gingival bleeding upon probing, teeth mobility and their potential loss in advanced stages. This review will evaluate the changes characterizing the oral microbiota in healthy periodontal tissues and those affected by periodontal disease through the evidence present in the literature. An important focus will be placed on the immediate and future impact of these changes on the modulation of the dysbiotic oral microbiome and clinical management of periodontal disease.

Gastroprotective effect of Lycium barbarum polysaccharides and C-phycocyanin in rats with ethanol-induced gastric ulcer

This study investigated the gastroprotective effect of Lycium barbarum polysaccharides (LBP) and C-phycocyanin (C-PC) in rats with ethanol-induced gastric ulcer. Rats were divided into 5 groups: normal, ulcer, ulcer treated with 100 mg/kg bw LBP, ulcer treated with 50 mg/kg bw C-PC, and ulcer treated with 50 mg/kg bw LBP and 25 mg/kg bw C-PC. Pretreatment with LBP and/or C-PC was given a week before ulcer induction. Ulcer induction was produced by 50% ethanol administration orally every other day for 4 weeks. After 5-week treatment, the histopathological observation showed that LBP or C-PC attenuated the severity of gastric mucosal damage. LBP decreased serum malondialdehyde (MDA) levels and gastric interleukin-6 (IL-6), intercellular adhesion molecule-1 (ICAM-1) levels, and myeloperoxidase (MPO) activity. C-PC decreased serum MDA levels and gastric tumor necrosis factor-α (TNF-α), IL-1β, IL-6, ICAM-1 levels, and MPO activity. Combined LBP and C-PC decreased serum MDA levels and gastric TNF-α, IL-1β, IL-6, and ICAM-1 levels. LBP and/or C-PC increased gastric heat shock protein 70 and non-protein sulfhydryl compounds. Rats with ulcer and treatment had enriched with the family Bacillaceae. Therefore, pretreatment with LBP and/or C-PC attenuated ethanol-induced gastric ulcer in rats via suppressing oxidation and inflammation and increasing gastroprotection.

Oral microbiome and health

The oral microbiome is diverse in its composition due to continuous contact of oral cavity with the external environment. Temperatures, diet, pH, feeding habits are important factors that contribute in the establishment of oral microbiome. Both culture dependent and culture independent approaches have been employed in the analysis of oral microbiome. Gene-based methods like PCR amplification techniques, random amplicon cloning, PCR-RELP, T-RELP, DGGE and DNA microarray analysis have been applied to increase oral microbiome related knowledge. Studies revealed that microbes from the phyla Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Fusobacteria, Neisseria, TM7 predominately inhabits the oral cavity. Culture-independent molecular techniques revealed the presence of genera Megasphaera, Parvimonas and Desulfobulbus in periodontal disease. Bacteria, fungi and protozoa colonize themselves on various surfaces in oral cavity. Microbial biofilms are formed on the buccal mucosa, dorsum of the tongue, tooth surfaces and gingival sulcus. Various studies demonstrate relationship between unbalanced microflora and development of diseases like tooth caries, periodontal diseases, type 2 diabetes, circulatory system related diseases etc. Transcriptome-based remodelling of microbial metabolism in health and disease associated states has been well reported. Human diets and habitat can trigger virus activation and influence phage members of oral microbiome. As it is said, "Mouth, is the gateway to the total body wellness, thus oral microbiome influences overall health of an individual".

Streptococcus pneumoniae Colonization Is Required To Alter the Nasal Microbiota in Cigarette Smoke-Exposed Mice

Smokers have nasal microbiota dysbiosis, with an increased frequency of colonizing bacterial pathogens. It is possible that cigarette smoke increases pathogen acquisition by perturbing the microbiota and decreasing colonization resistance. However, it is difficult to disentangle microbiota dysbiosis due to cigarette smoke exposure from microbiota changes caused by increased pathogen acquisition in human smokers. Using an experimental mouse model, we investigated the impact of cigarette smoke on the nasal microbiota in the absence and presence of nasal pneumococcal colonization. We observed that cigarette smoke exposure alone did not alter the nasal microbiota composition. The microbiota composition was also unchanged at 12 h following low-dose nasal pneumococcal inoculation, suggesting that the ability of the microbiota to resist initial nasal pneumococcal acquisition was not impaired in smoke-exposed mice. However, nasal microbiota dysbiosis occurred as a consequence of established high-dose nasal pneumococcal colonization at day 3 in smoke-exposed mice. Similar to clinical reports on human smokers, an enrichment of potentially pathogenic bacterial genera such as Fusobacterium, Gemella, and Neisseria was observed. Our findings suggest that cigarette smoke exposure predisposes to pneumococcal colonization independent of changes to the nasal microbiota and that microbiota dysbiosis observed in smokers may occur as a consequence of established pathogen colonization.

Visual programming for next-generation sequencing data analytics

Background

High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a ‘cultural’ gap between the end user and the developer.

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Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter. Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics. An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent), interoperable (with external software interface), and usable (via an intuitive graphical user interface). These characteristics should facilitate both the run of standardized NGS pipelines and the development of new workflows based on technological advancements or users’ needs. We discuss in detail the potential of a computational framework blending generic template programming and visual programming that addresses all of the current limitations.

Conclusion

In the long term, a proper, well-developed (although not necessarily unique) software framework will bridge the current gap between data generation and hypothesis testing. This will eventually facilitate the development of novel diagnostic tools embedded in routine healthcare.

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB

We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.

Polymicrobial community-acquired pneumonia: An emerging entity

Polymicrobial aetiology in community-acquired pneumonia (CAP) is more common than previously recognized. This growing new entity can influence inflammation, host immunity and disease outcomes in CAP patients. However, the true incidence is complicated to determine and probably underestimated due mainly to many cases going undetected, particularly in the outpatient setting, as the diagnostic yield is restricted by the sensitivity of currently available microbiologic tests and the ability to get certain types of clinical specimens. The observed rate of polymicrobial cases may also lead to new antibiotic therapy considerations. In this review, we discuss the pathogenesis, microbial interactions in pneumonia, epidemiology, biomarkers and antibiotic therapy for polymicrobial CAP.