The Protein Paradox: Elucidating the Complex Nutritional Ecology of the Invasive Berry Pest, Spotted-Wing Drosophila (Diptera: Drosophila suzukii)

Spotted-wing drosophila (SWD), Drosophila suzukii, has become one of the most widely studied insect species over the last decade, largely due to its recent invasion and rapid expansion across the Americas and Europe. Unlike other drosophilid species, which colonize rotting fruit, SWD females possess a serrated ovipositor that allows them to lay eggs in intact ripening fruit, causing significant economic problems for fruit/berry producers worldwide. Though an impressive amount of research has been conducted on SWD's ecology and physiology, aspects of their nutritional ecology remain ambiguous. This review synthesizes the research to date to provide a more comprehensive view of SWD's nutritional relationship with its fruit hosts and associated microbes. Overall, data suggest that SWD's ability to utilize novel resources is likely due to changes in their ecological, rather than physiological, niche that are largely mediated by microbial associations. Studies show that SWD's nutrient intake is comparable to other drosophilid species, indicating limited adaptation to feeding on lower-protein resources. Instead, data show that fruit protein content is a reliable predictor of host suitability and that fruit-microbe dynamics have a strong impact on protein availability. In particularly, fruit protein increases after infestation with SWD-associated microbes, suggesting that initially-suboptimal intact fruits can become protein-rich on a timeframe that is relevant for larval nutrition. This body of work suggests that microbial associations between flies and their fruit hosts can compensate for the nutritional differences between intact and rotting fruit, and that these relationships are likely responsible for SWD's expanded nutritional niche.

Microbial Communities Associated With Stunted Growth Syndrome In Penaeus Vannamei Farming

Purpose: Stunted/slow growth syndrome is one of the yield-limiting diseases in Penaeus vannamei farming. Limited information is available on the aetiology of this condition, which needs to be studied to devise prophylactic measures to minimise the production losses. Amongst the factors that influence this condition, microbial communities in the growing environment play an important role. This study aimed at understanding major microbial associations of affected and healthy pond waters through shotgun metagenomics.Method: The water samples were filtered through vacuum filtration to extract suspended microbes. Subsequently, DNA was isolated from the filtrate using PowerSoil® DNA Isolation Kit. Libraries prepared from isolated DNA were sequenced using the shotgun metagenomic method on the Illumina HiSeq platform. The microbial profiling and their functional prediction of the shotgun metagenome sequences were carried out using stand-alone versions of Kaiju, OmicsBox respectively. Results: The taxonomic classification results revealed that species of Oceanospirillum, and vibrio were high in the disease sample, while Rhodobacteraceae bacterium and Neptunomonas were high in the healthy sample. The alpha diversity analysis showed slightly higher diversity in the healthy sample compared to the disease infected. The taxonomic biomarkers for healthy and infected states reported in previous studies were also observed in this study. The major functional associations of both the healthy and infected groups include amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, and energy production and conversion. Conclusion: The study identified major taxonomical and functional associations of ponds affected and unaffected with stunted growth syndrome. These associations significantly varied between the samples, indicating dysbiosis of the microbial profiles in the pond waters. This dysbiosis could be a potential cause for the manifestation of stunted growth syndrome. Microbial associations along with other pond environmental factors need to be further explored for an in-depth understanding of stunted growth syndrome.

The state of the microflora of prostate secretions in healthy individuals and in acute bacterial prostatitis

Relevance. Acute bacterial prostatitis is one of the urgent problems in urology. According to the data presented in the literature, the number of men who have been diagnosed with this disease ranges from 10 to 40 %. At the same time, the main etiological factor in the development of this pathology is most often assigned to the bacterial microflora. However, most of the works are devoted to the study of the microflora in chronic prostatitis, and the state of the microflora in acute bacterial prostatitis remains insufficient. The aim of the study is to evaluate the state of prostate secretion microflora in a comparative aspect in healthy individuals and in patients with acute bacterial prostatitis. Materials and Methods. The study included a comparative analysis of microbiological cultures in prostate secretion of 30 people. All examined were divided into two groups: the first included 15 people without established urological pathology, the second - 15 people with an established diagnosis of acute bacterial prostatitis. Results and Discussion. As a result of the study, it was found that when sowing prostate secretion in persons without established pathology, the absence of microorganism growth was not observed in 60 % of observations, while in 40 % of cases, microorganisms growth was obtained. In the group of examined without established urological pathology, the growth of microorganisms of the following was noted: Escherichia coli - in 58 % of observations; Staphylococcus epidermidis - in 10 % of observations; Staphylococcus warnerii - in 6 % cases and Enterobacter spp. - in 26 %. At the same time, the number of detected microorganisms did not exceed 104 CFU/ml. At the same time, the presence of microbial associations was not recorded. In patients with acute bacterial prostatitis, the sterile prostate secret was 13,3 %, and in 86,7 % of people, microflora growth was obtained. Most often, in the group examined with acute bacterial prostatitis, Escherichia coli was obtained - in 45 % of the observations; Klebsiella spp. - in 23 % cases and Proteus spp. - in 19 %. Less often Staphylococcus epidermidis - in 8 % of observations; Enterobacter spp. - 3,2 %. Serratia spp. - 1,1 % and Staphylococcus warnerii - in 0,7 % cases were the least obtained. At the same time, 86 % of observations in this group revealed microbial associations. Conclusion . Comparison of the state of microflora of prostate secretions in healthy individuals and patients with acute bacterial prostatitis revealed that in patients with acute bacterial prostatitis, the absence of inoculated microflora in prostate secretions was 3 times less than in healthy individuals (13.3 % and 40 %, respectively.), and Escherichia coli was the most common microorganism in the group of patients with acute bacterial prostatitis.

Microbial associations of shallow-water Mediterranean marine cave Solenogastres (Mollusca)

The first cave-dwelling Solenogastres—marine shell-less worm-like mollusks—were sampled from Mediterranean marine caves floor silt in the Marseille area. The mollusks were 1.5 mm in length, had a transparent body with shiny spicules and appear to represent a new Tegulaherpia species. Electron microscopy revealed a high number of microbial cells, located on the surface of the spicules as well as in the cuticle of Tegulaherpia sp. The observed microbial cells varied in morphology and were unequally distributed through the cuticle, reaching a highest density on the dorsal and lateral sides and being practically absent on the ventral side. Next Generation Sequencing (NGS) of V4 region of 16S rRNA gene amplicons, obtained from the DNA samples of whole bodies of Tegulaherpia sp. revealed three dominating microorganisms, two of which were bacteria of Bacteroidetes and Nitrospirae phyla, while the third one represented archaea of Thaumarchaeota phylum. The Operational Taxonomic Unit (OTU), affiliated with Bacteroidetes was an uncultured bacteria of the family Saprospiraceae (93–95% of Bacteroidetes and 25–44% of the total community, depending on sample), OTU, affiliated with Nitrospirae belonged to the genus Nitrospira (8–30% of the community), while the thaumarchaeal OTU was classified as Candidatus Nitrosopumilus (11–15% of the community). Members of these three microbial taxa are known to form associations with various marine animals such as sponges or snails where they contribute to nitrogen metabolism or the decomposition of biopolymers. A similar role is assumed to be played by the microorganisms associated with Tegulaherpia sp.

Microbial associations with Microscopic Colitis

BACKGROUND AND OBJECTIVE: Microscopic colitis is a relatively common cause of chronic diarrhea and may be linked to luminal factors. Given the essential role of the microbiome in human gut health, analysis of microbiome changes associated with microscopic colitis could provide insights into the development of the disease. METHODS: We enrolled patients who underwent colonoscopy for diarrhea. An experienced pathologist classified patients as having microscopic colitis (n=52) or controls (n=153). Research biopsies were taken from the ascending and descending colon, and the microbiome was characterized with Illumina sequencing. We analyzed the associations between microscopic colitis and microbiome with a series of increasingly complex models adjusted for a range of demographic and health factors. RESULTS: We found that alpha-diversity was significantly lower in microscopic colitis cases compared to controls in the descending colon microbiome. In the descending colon, a series of models that adjusted for an increasing number of co-variates found taxa significantly associated with microscopic colitis, including Proteobacteria that was enriched in cases and Collinsella enriched in controls. While the alpha-diversity and taxa were not significantly associated with microscopic colitis in the ascending colon microbiome, the inference p-values based on ascending and descending microbiomes were highly correlated. CONCLUSION: Our study demonstrates an altered microbiome in microscopic colitis cases compared to controls. Because both the cases and controls had diarrhea, we have identified candidate taxa that could be mechanistically responsible for the development of microscopic colitis independent of changes to the microbial community caused by diarrhea.

The role of microorganism association in the development of chronic purulent maxillary sinusitis in patients with type 1 diabetes mellitus

Aim – to study the species composition and population level of the microbiota of the content of the maxillary sinuses and the role of associations of microorganisms in the development and course of chronic purulent maxillary sinusitis (CPMS) in patients with type 1 diabetes.Material and methods. A microbiological examination of 97 samples of the contents of the cavity of the maxillary sinuses was carried out. The main group consisted of 50 patients with CPMS with type 1 diabetes at the age of 20-67 years (10 patients at the age of 20-31 years, 14 patients - 31-45 years old and 26 - at the age of 45-67 years). Among the patients of the main group, endocrinologists established the course of type 1 diabetes mellitus of moderate severity in 39 patients, and a severe course in 11 patients. The control group consisted of 47 CPMS patients of the same age without type 1 diabetes mellitus (DM).Results. Bacteriological and mycological methods in the content of maxillary sinuses of patients with maxillary sinusitis associated with type 1 diabetes mellitus (DM) 175 strains of different kinds of microorganisms were isolated and identified, belonging to 24 various taxonomic groups which form different by their qualitative content microbial associations in the biotope which consist of three different kinds in 58% of patients, consist of four kinds – in 34,0% and five various taxa – in 8,0% of patients. Chronic purulent maxillary sinusitis in patients with type 1 DM disrupts microbial associations. In patients with CPMS with type 1 DM in comparison with the control group, the number of associations consist of three kinds increases by 2,7 times, but the number of associations composed of 4 types of microorganisms decreases by 11.76%. The number of associations consisting of 5 types in patients is reduced by 3.5 times. The above may indicate the influence of not only the etiological agent but also a certain association of microorganisms on the severity of the course of CPMS associated with type 1 diabetes. All leading pathogens persist in the biotope in association. Associates, depending on their role in normobiocenosis, can inhibit the pathogenetic activity of the leading pathogen or, conversely, activate its pathogenetic role, which must be taken into account when choosing a therapeutic tactics.Conclusions. Chronic purulent maxillary sinusitis in patients with type 1 diabetes disrupts microbial associations. In the content of the cavity of the maxillary sinuses of patients with chronic purulent maxillary sinusitis, combined with type 1 diabetes mellitus, 175 strains of various types of microorganisms belonging to 24 different taxonomic groups were isolated and identified, which in the biotope form microbial associations of different qualitative composition, consisting of 3 different species in 58% of patients, out of 4 species in 34.0% and from five different taxa - in 8.0% of patients. Among the most numerous associations, consisting of 3 types of pathogenic and opportunistic autochthonous facultative microorganisms, associations of the following representatives are more common: M. catarrhalis, S. aureus and Bacteroides spp.; Prevotella spp., S. viridans and S. salivarius; M. catarrhalis, Prevotella spp. and S. epidermitidis; H. influenzae, Prevotella spp. and S. epidermitidis. Associations consisting of 4 species were found in 34% of patients and consist of S. pneumoniae, M. catarrhalis, S. pyogenes, Fusobacterium spp; S. pneumoniae, E. coli, S. aureus and Candida spp.; S. pneumoniae, E. coli Hly +, S. viridans and Candida spp. In patients with chronic purulent maxillary sinusitis, combined with type 1 diabetes mellitus with a severe course, there were associations consisting of S. pneumoniae, M. catarrhalis, Candida spp. and S. epidermitidis; S. pneumoniae, M. catarrhalis, S. pyogenes, S. epidermitidis; Bacteroides spp., H. influenzae, S. pyogenes, Enterobacter freundii spp.; Bacteroides spp., H. influenzae, S. pyogenes, Candida spp. In patients with chronic purulent maxillary sinusitis, against the background of a severe course of type 1 diabetes mellitus, associations of microorganisms, consisting of 5 types, were found. Their composition was different, but in all the pathogen S. pneumoniae was isolated and identified at a high population level, opportunistic obligate anaerobic bacteria of the genus Bacteroides and Prevotella, Fusobacterium, streptococci, and Staphylococcus aureus. All leading pathogens persist in the biotope in association, which must be taken into account when choosing therapeutic tactics.

Insights into Oropharyngeal Microbiota, Biofilms and Associated Diseases from Metagenomics and Transcriptomic Approaches

Oral cavity is an ecologically complex environment and hosts a diverse microbial community. Most of these organisms are commensals, however, on occasion, some have the potential to become pathogenic causing damage to the human host. Complex interactions between pathogenic bacteria, the microbiota, and the host can modify pathogen physiology and behavior. Most bacteria in the environment do not exist in free-living state but are found as complex matrix enclosed aggregates known as biofilms. There has been research interest in microbial biofilms because of their importance in industrial and biomedical settings. Bacteria respond to environmental cues to fine-tune the transition from planktonic growth to biofilm by directing gene expression changes favorable for sessile community establishment. Meta-approaches have been used to identify complex microbial associations within human oral cavity leading to important insights. Comparative gene expression analysis using deep sequencing of RNA and metagenomics studies done under varying conditions have been successfully used in understanding and identifying possible triggers of pathogenicity and biofilm formation in oral commensals.

The Sputum Microbiome in Pulmonary Tuberculosis and Its Association With Disease Manifestations: A Cross-Sectional Study

Each day, approximately 27,000 people become ill with tuberculosis (TB), and 4,000 die from this disease. Pulmonary TB is the main clinical form of TB, and affects the lungs with a considerably heterogeneous manifestation among patients. Immunomodulation by an interplay of host-, environment-, and pathogen-associated factors partially explains such heterogeneity. Microbial communities residing in the host's airways have immunomodulatory effects, but it is unclear if the inter-individual variability of these microbial communities is associated with the heterogeneity of pulmonary TB. Here, we investigated this possibility by characterizing the microbial composition in the sputum of 334 TB patients from Tanzania, and by assessing its association with three aspects of disease manifestations: sputum mycobacterial load, severe clinical findings, and chest x-ray (CXR) findings. Compositional data analysis of taxonomic profiles based on 16S-rRNA gene amplicon sequencing and on whole metagenome shotgun sequencing, and graph-based inference of microbial associations revealed that the airway microbiome of TB patients was shaped by inverse relationships between Streptococcus and two anaerobes: Selenomonas and Fusobacterium. Specifically, the strength of these microbial associations was negatively correlated with Faith's phylogenetic diversity (PD) and with the accumulation of transient genera. Furthermore, low body mass index (BMI) determined the association between abnormal CXRs and community diversity and composition. These associations were mediated by increased abundance of Selenomonas and Fusobacterium, relative to the abundance of Streptococcus, in underweight patients with lung parenchymal infiltrates and in comparison to those with normal chest x-rays. And last, the detection of herpesviruses and anelloviruses in sputum microbial assemblage was linked to co-infection with HIV. Given the anaerobic metabolism of Selenomonas and Fusobacterium, and the hypoxic environment of lung infiltrates, our results suggest that in underweight TB patients, lung tissue remodeling toward anaerobic conditions favors the growth of Selenomonas and Fusobacterium at the expense of Streptococcus. These new insights into the interplay among particular members of the airway microbiome, BMI, and lung parenchymal lesions in TB patients, add a new dimension to the long-known association between low BMI and pulmonary TB. Our results also drive attention to the airways virome in the context of HIV-TB coinfection.

The choice of antibacterial drugs in dentistry taking into account the oral microbiome

The article presents modern data on the features of the oral microbiome and its medical significance when prescribing systemic antibacterial therapy for infectious and inflammatory processes in the oral cavity. The main microbial associations in normal conditions, as well as in diseases of periodontal tissues and apical periodontitis are presented. The use of antibacterial drugs in dentistry is aimed at eliminating the etiological factor of the pathogenic microflora of the oral cavity. The effectiveness of the treatment depends on how well the doctor aware of the main pathogens and microbial associations in generalized periodontitis, periodontitis, a choice of optimal antibacterial agent, compliance with indications and contraindications upon treatment.