Microbiome in Ecosystem

While dietary supplements can have beneficial effects on the health of the intestine, these effects can come with unresolved issues in terms of therapeutic efficacy and mechanisms of action. In this study, the model probiotic Lacticaseibacillus rhamnosus GG ATCC 53103 and the anciently used dietary supplement Limnospira indica strain PCC 8005 were compared for their effects on murine intestinal ecology. Healthy male mice received either saline or suspensions of living cells of L. indica PCC 8005 or L. rhamnosus GG daily along a two-week intervention period, followed by a two-week washout period. Both bacteria-based solutions appeared able to transiently shift the microbial community, which were characterized by a higher relative abundance of members of the butyrate producing Lachnospiraceae and Porphyromonadaceae families. Full article

A culture-independent mycobiome survey in Haplic Cambisol under Korean pine in a long-term field experiment in the Russian Far East was conducted using sequence analysis of the ITS region amplified with ITS3/ITS4 primers using the metagenomic DNA as a matrix. Overall 758 fungal OTUs were identified, representing 15 phyla, 47 classes, 104 orders, 183 families, and 258 genera. More OTUs represented the Ascomycota phylum (513) than Basidiomycota (113), with both phyla together comprising 95% of the relative abundance. The Leotiomycetes class was ultimately prevailing; apparently contributing significantly to the organic matter decomposition and microbial biomass in soil, as shown by a PCA. Only two dominant OTUs (Pseudogymnoascus sp. and Hyaloscyphaceae, both Ascomycota) were common in the studied samples. The presented high mycobiome diversity in soil under the monospecies artificial forest, where Korean pine had been the sole edificator for forty years, allows concluding that plant chemistry diversity is the main factor shaping the soil mycobiome in such an environment. The obtained data provide a reference for further studies of soil mycobiota, especially under Korean pine with its aesthetic, as well as nut-producing, potential. The results can be helpful in the targeted creating of a soil mycobiome beneficial for pines in afforestation and remediation contexts. Full article

Mosquito-borne arboviruses, such as dengue virus, West Nile virus, Zika virus and yellow fever virus, impose a tremendous cost on the health of populations around the world. As a result, much effort has gone into the study of the impact of these viruses on human infections. Comparatively less effort, however, has been made to study the way these viruses interact with mosquitoes themselves. As ingested arboviruses infect their midgut and subsequently other tissue, the mosquito mounts a multifaceted innate immune response. RNA interference, the central intracellular antiviral defense mechanism in mosquitoes and other invertebrates can be induced and modulated through outside triggers (small RNAs) and treatments (transgenesis or viral-vector delivery). Accordingly, modulation of this facet of the mosquito’s immune system would thereby suggest a practical strategy for vector control. However, this requires a detailed understanding of mosquitoes’ endogenous small RNAs and their effects on the mosquito and viral proliferation. This paper provides an up-to-date overview of the mosquito’s immune system along with novel data describing miRNA profiles for Aedes aegypti and Culex quinquefasiatus in Grenada, West Indies. Full article

Microbial lipase is one of the major sources of the enzyme that has been broadly exploited in the food, detergent, and pharmaceutical industries due to its high catalytic activity, high yield, and environmental friendliness and cost-effectiveness. Therefore, the aim of this study was to optimize the medium for the submerged fermentation for lipase production by a novel strain, Bacillus salmalaya strain 139SI. The media subjected to lipase production was Luria Bertani (LB) with different carbon sources and surfactants supplemented to determine which would give the highest lipase activity of Bacillus salmalaya. The Lipase activity of the supernatant containing lipase enzyme was ddetermined using the titrimetric method with hydrolysis reaction. Results showed that the olive oil that was used as a carbon source, induced the highest lipase activity (11.0 U/mL) compared to sunflower oil (9.6 U/mL) and cooking oil waste (7.8 U/mL). For surfactants, LB medium supplemented with tween 80 enhanced higher lipase activity (6.8 U/mL) compared to tween 20 (6.0 U/mL) and sodium dodecyl sulphate (SDS) (2.0 U/mL). Thus, it can be concluded that submerged fermentation allows optimization of the culture medium whereby, among carbon sources, olive oil induced the highest lipase production, whereas Tween 80 was the best lipase inducer compared to other surfactants. Full article

Due to the importance of microbes in soil health and crop production, manipulation of microbiomes provides a new strategy for improving crop growth and agricultural ecosystems. Current understanding is limited regarding the responses of soil and crop endophytic microbiomes to field management and microbiome programming. In this study, we investigated soil and tea root bacterial communities under conventional and organic cropping systems using 16S rRNA gene sequencing. A significant difference in soil and root bacterial community structure was observed under different field managements, leading to 43% and 35% variance, respectively. We also identified field management-sensitive species both in soils and tea roots that have great potential as bioindicators for bacterial microbiome manipulation. Moreover, through functional profile predictions of microbiomes, xenobiotics degradation in soil bacterial communities is enriched in organic farms, suggesting that biodegradation capabilities are enhanced under organic cropping systems. Our results demonstrate the effects of field management on both soil and tea root bacterial microbiomes and provide new insights into the reprogramming of microbial structures. Full article

Sea urchins, in many instances, are collected from the wild, maintained in the laboratory aquaculture environment, and used as model animals for various scientific investigations. It has been increasingly evident that diet-driven dysbiosis of the gut microbiome could affect animal health and physiology, thereby impacting the outcome of the scientific studies. In this study, we compared the gut microbiome between naturally occurring (ENV) and formulated diet-fed laboratory aquaculture (LAB) sea urchin Lytechinus variegatus by amplicon sequencing of the V4 region of the 16S rRNA gene and bioinformatics tools. Overall, the ENV gut digesta had higher taxa richness with an abundance of Propionigenium, Photobacterium, Roseimarinus, and Flavobacteriales. In contrast, the LAB group revealed fewer taxa richness, but noticeable abundances of Arcobacter, Agarivorans, and Shewanella. However, Campylobacteraceae, primarily represented by Arcobacter spp., was commonly associated with the gut tissues of both ENV and LAB groups whereas the gut digesta had taxa from Gammaproteobacteria, particularly Vibrio spp. Similarly, the co-occurrence network displayed taxonomic organizations interconnected by Arcobacter and Vibrio as being the key taxa in gut tissues and gut digesta, respectively. Predicted functional analysis of the gut tissues microbiota of both ENV and LAB groups showed a higher trend in energy-related metabolisms, whereas amino acids, carbohydrate, and lipid metabolisms heightened in the gut digesta. This study provides an outlook of the laboratory-formulated diet-fed aquaculture L. variegatus gut microbiome and predicted metabolic profile as compared to the naturally occurring animals, which should be taken into consideration for consistency, reproducibility, and translatability of scientific studies. Full article

Acute otitis media (AOM) constitutes a multifactorial disease, as several host and environmental factors contribute to its occurrence. Prevention of AOM represents one of the most important goals in pediatrics, both in developing countries, in which complications, mortality, and deafness remain possible consequences of the disease, compared to in developed countries, in which this condition has an important burden in terms of medical, social, and economical implications. The strategies for AOM prevention are based on reducing the burden of risk factors, through the application of behavioral, environmental, and therapeutic interventions. The introduction of culture-independent techniques has allowed high-throughput investigation of entire bacterial communities, providing novel insights into the pathogenesis of middle ear diseases through the identification of potential protective bacteria. The upper respiratory tract (URT) is a pivotal region in AOM pathogenesis, as it could act as a source of pathogens than of protective microorganisms for the middle ear (ME). Due to its direct connection with the external ambient, the URT is particularly exposed to the influence of environmental agents. The aim of this review was to evaluate AOM environmental risk factors and their impact on URT microbial communities, and to investigate AOM pathogenesis from the microbiota perspective. Full article

The introduction of next generation sequencing techniques has enabled the characterization of the urinary tract microbiome, which resulted in the rejection of the long-held notion of urinary bladder sterility. Since the discovery and confirmation of the human bladder microbiome, an increasing number of studies have defined this microbial community and understand better its relationship to urinary pathologies. The composition of microbial communities in the urinary tract is linked to a variety of urinary diseases. The purpose of this review is to provide an overview of current information about the urinary microbiome and diseases as well as the development of novel treatment methods. Full article

The aim of this review was to investigate the effectiveness of the Human Oral Microbe Identification Microarray (HOMIM) in identifying and quantifying bacterial species of the oral microbiome in periodontal disease. The search for articles was conducted in CENTRAL, CINAHL, MEDLINE and EMBASE by two reviewers, and included articles published in English between January 1990 and December 2021. The selected articles were human observational studies in adults between 18 and 65 years, presenting specific predefined keywords. Articles were initially selected by title and abstract; articles that met the inclusion criteria were analyzed for methodological quality using a detailed checklist for quality assessment. Data were extracted and reported using the PRISMA tool. The study design, sample, follow-up period, collection and microbial analysis methods, statistical treatment, results and discussion were quality assessed and risk of bias was evaluated using the Cochrane Risk-of-Bias tool. A narrative synthesis approach was used to synthesize and interpret the extracted data. From the initial search, 2931 articles were retrieved; 51 of these were then selected after screening by title and abstract. Subsequently, 8 articles met the inclusion after full-text reading and were classed according to methodological quality as high (2), moderate (3) or low (3). Studies included in this review were of high and medium quality. Data from the Human Oral Microbe Identification Microarray (HOMIM) provide much more robust results, showing major shifts between periodontal health and periodontal disease. Compared to earlier techniques such as Denaturing Gradient Gel Electrophoresis (DGGE), HOMIM represents a more effective approach for quantification due to its high sensitivity; thus, it is able to identify a high prevalence of periodontal pathogens and novel species in low abundance. The literature provides moderate evidence that the Human Oral Microbe Identification Microarray (HOMIM) is more effective in identifying and quantifying bacterial species of the oral microbiome in periodontal disease, compared to earlier molecular and non-molecular methods such as Denaturing Gradient Gel Electrophoresis (DGGE) and a culture-based approach with phenotypic tests. Full article