Community Of Microorganisms Research Articles

Can Genomics of Gut Microbiota in Stool Samples be Analysed by MERLIN?

Metagenomics is important for studying microorganisms that live in microbial communities, particularly those inhabiting the human body. For instance, the gut microbiota is a community of microorganisms that reside in the human gut and interact with humans through secondary metabolites. These metabolites produced by the gut microbiota are extremely important and serve as precursors for various human needs, such as short chain fatty acids (SCFA). While there have been reports of functional secondary metabolites produced by different gut microbiota, none have been utilized on the Merlin platform. In this article, we will examine how the Merlin platform can analyze the gut microbiota community. Metabolic Models Reconstruction using Genome-Scale Information (MERLIN) is a bioinformatics tool that can analyze the functional microbial community as well as the taxonomy of these bacteria.

Liquid infused silicon based urinary catheters: A simple laboratory model to study bacterial biofilm formation

Biofilms are organized communities of micro-organisms buried firmly on an extra polymeric matrix attached to the living surface. The matrix which is formed surrounding the bacteria makes them tolerant to harsh environmental conditions as well as resistant to antibacterial treatment. The development of biofilms in clinical or hospital settings is the major reason for several infections. They have a negative impact when they are formed on medical devices as it is difficult to eradicate them using disinfectants or antibiotics available. Several in vitro models have been implemented in the last decade to evaluate antimicrobial activity on bacterial biofilms. Although well-established static biofilm methods are available; there is a lack of simple dynamic biofilm models to replicate the clinical settings of biofilm development. In this scenario, considering the importance of this research area, we planned to design laboratory-scale working models to study biofilms. We used Pseudomonas aeruginosa as a model organism. We divided the biofilm models into two categories namely static and dynamic models. The dynamic model of biofilm, that we used for mimicking the clinical setting, was a silicone-based catheter model. This new model will contribute to deeper knowledge about the physiology, structure, formation, and composition of biofilms. This method can be used as an appropriate and up-to-date technique to study biofilms in laboratory settings.

Association between flavors and microbial communities of traditional Aspergillus-Douchi produced by a typical industrial-scale factory

Aspergillus-Douchi is a traditional fermentation food which possesses unique flavors caused by diverse microbiota in fermentation ecosystems. However, the correlations between flavor characteristics and microorganism succession are rarely researched. In this research, flavors and microorganism community (bacterial and fungal) of Douchi at different koji-making and post-fermentation stages were analyzed by SDE-GC-MS and 16S rRNA sequencing, respectively. Moreover, an association between flavor formation and microorganism succession was analyzed by Pearson analytical methods. Results showed that aldehydes, ketones and aromatic compounds were the primary flavors during koji-making. In the post-fermentation, the main flavors became acids, esters, aromatic compounds and alcohols, as well as many new elements, including hexadecenoic acid ethyl palmitate and 9,12-octadecadie methyl linoleate. In microorganism community, the dominant microorganisms were bacteria, including Bacillus velezensis, Bacillus licheniformis, Staphylococcus gallinarum, Staphylococcus saprophyticus and Pediococcus acidilactici. Aspergillaceae was only dominant fungal on the surface and inside Douchi throughout fermentation, with a relative abundance of over 40%. Bacillus velezensis were involved in synthesizing a wide variety of volatiles during koji-making, while Staphylococcus and Debaryomycetaceae were closely related to the flavor formation throughout post-fermentation. Conclusively, the aromatic flavors in Aspergillus-Douchi were mainly produced from the synergistic actions of bacteria (Bacillus and Staphylococcus) and fungi (Debaryomycetaceae).

Impact of fungi on historical monument with reference to Mahadev temple Bastar of Chhatisgarh

Materials of built heritage are at risk of bio-deterioration caused by diverse populations of microorganisms living in biofilms. The microbial metabolites of these biofilms are responsible for the deterioration of the underlying substratum and may lead to physical weakening and discoloration of stone. Fungal ability in production of pigments and organic acids have crucial role in discoloration and degradation of different types of stone in cultural heritage objects. Additionally, stone objects may support novel communities of microorganism that are active in bio-deterioration process this investigation focused on mycological analyses of microbial biofilm from Mahadev temple, Bastar of Chhattisgarh state which is made of sand stone and which were heavily colonized by fungi. The eight fungal species on sand stone were isolated. Aspergillus sp. was common in stone structure. The identified micro fungi cause discoloration as well as mechanical exfoliation of building stone material that was analyzed through mechanical hyphae penetration and production of dark pigments and organic acids.

Plant species shape the bacterial communities on the phyllosphere in a hyper-arid desert

Microorganisms are an important component of global biodiversity. However, they are vulnerable to hyper-arid climates in desert regions. Xerophytes are desert vegetation with unique biodiversity. However, little is known about the identities and communities of phyllosphere epiphytic microorganisms inhabiting the xerophyte leaf surface in the hot and dry environment. The diversity and community composition of phyllosphere epiphytes on different desert plants in Gansu, China, was investigated using the next-generation sequencing technique, revealing the diversity and community composition of the phyllosphere epiphytic bacteria associated with desert xerophytes. In addition, the ecological functions of the bacterial communities were investigated by combining the sequence classification information and prokaryotic taxonomic function annotation (FAPROTAX). This study determined the phyllosphere bacterial community composition, microbial interactions, and their functions. Despite harsh environments in the arid desert, we found that there are still diverse epiphytic bacteria on the leaves of desert plants. The bacterial communities mainly included Actinobacteria (52.79%), Firmicutes (31.62%), and Proteobacteria (12.20%). Further comparisons revealed different microbial communities, including Firmicutes at the phylum and Paenibacillaceae at the family level, in the phyllosphere among different plants, suggesting that the host plants had strong filter effects on bacteria. Co-occurrence network analysis revealed positive relationships were dominant among different bacterial taxa. The abundance of Actinobacteria and Proteobacteria was positively correlated, demonstrating their mutual relationship. On the other hand, the abundance of Firmicutes was negatively correlated, which suggested that they inhibit the growth of other bacterial taxa. FAPROTAX prediction revealed that chemoheterotrophy (accounting for 39.02% of the community) and aerobic chemoheterotrophy (37.01%) were the main functions of the leaf epiphytic bacteria on desert plants. This study improves our understanding of the community composition and ecological functions of plant-associated microbial communities inhabiting scattered niches in the desert ecosystem. In addition, the study provides insight into the biodiversity assessment in the desert region.

Current concepts of the intestinal microbiota and prospects for microbiocenosis adjustment: A review

The review presents current data on the interaction between the human body and the community of microorganisms inhabiting its gastrointestinal tract. The terminology and methods for analyzing quantitative and qualitative characteristics of gut microbiota are presented. The review also focuses on the concepts of eubiosis, dysbiosis, and the possibilities of correcting dysbiosis with probiotics and probiotic foods.

The lung, the niche, and the microbe: Exploring the lung microbiome in cancer and immunity.

The lung is a complex and unique organ system whose biology is strongly influenced by environmental exposure, oxygen abundance, connection to extrapulmonary systems via a dense capillary network, and an array of immune cells that reside in the tissue at steady state. The lung also harbors a low biomass community of commensal microorganisms that are dynamic during both health and disease with the capacity to modulate regulatory immune responses during diseases such as cancer. Lung cancer is the third most common cancer worldwide with the highest mortality rate amongst cancers due to the difficulty of an early diagnosis. This review discusses the current body of work addressing the interactions between the lung microbiota and the immune system, and how these two components of the pulmonary system are linked to lung cancer development and outcomes. Bringing in lessons from broader studies examining the effects of the gut microbiota on cancer outcomes, we highlight many challenges and gaps in this nascent field.

Impact of Data and Study Characteristics on Microbiome Volatility Estimates.

The human microbiome is a dynamic community of bacteria, viruses, fungi, and other microorganisms. Both the composition of the microbiome (the microbes that are present and their relative abundances) and the temporal variability of the microbiome (the magnitude of changes in their composition across time, called volatility) has been associated with human health. However, the effect of unbalanced sampling intervals and differential read depth on the estimates of microbiome volatility has not been thoroughly assessed. Using four publicly available gut and vaginal microbiome time series, we subsampled the datasets to several sampling intervals and read depths and then compared additive, multiplicative, centered log ratio (CLR)-based, qualitative, and distance-based measures of microbiome volatility between the conditions. We find that longer sampling intervals are associated with larger quantitative measures of change (particularly for common taxa), but not with qualitative measures of change or distance-based volatility quantification. A lower sequencing read depth is associated with smaller multiplicative, CLR-based, and qualitative measures of change (particularly for less common taxa). Strategic subsampling may serve as a useful sensitivity analysis in unbalanced longitudinal studies investigating clinical associations with microbiome volatility.

Label-free sub-micrometer 3D imaging of ciprofloxacin in native-state biofilms with cryo-time-of-flight secondary ion mass spectrometry

High spatial resolution mass spectrometry imaging has been identified as a key technology needed to improve understanding of the chemical components that influence antibiotic resistance within biofilms, which are communities of micro-organisms that grow attached to a surface. Time-of-flight secondary ion mass spectrometry (ToF–SIMS) offers the unique ability for label-free 3D imaging of organic molecules with sub-micrometer spatial resolution and high sensitivity. Several studies of biofilms have been done with the help of ToF–SIMS, but none of those studies have shown 3D imaging of antibiotics in native-state hydrated biofilms with cell-level resolution. Because ToF–SIMS measurements must be performed in a high-vacuum environment, cryogenic preparation and analysis are necessary to preserve the native biofilm structure and antibiotic spatial distribution during ToF–SIMS measurements. In this study, we have investigated the penetration of the antibiotic ciprofloxacin into Bacillus subtilis biofilms using sub-micrometer resolution 3D imaging cryo-ToF–SIMS. B. subtilis biofilms were exposed to physiologically relevant levels of ciprofloxacin. The treated biofilms were then plunge-frozen in liquid propane and analyzed with ToF–SIMS under cryogenic conditions. Multivariate analysis techniques, including multivariate curve resolution (MCR) and inverse maximum signal factor (iMSF) denoising, were used to aid analysis of the data and facilitate high spatial resolution 3D imaging of the biofilm, providing individually resolved cells and spatially resolved ciprofloxacin intensity at “real world” concentrations.Graphical

The Oral Microbiota in Valvular Heart Disease: Current Knowledge and Future Directions.

Oral microbiota formation begins from birth, and everything from genetic components to the environment, alongside the host's behavior (such as diet, smoking, oral hygiene, and even physical activity), contributes to oral microbiota structure. Even though recent studies have focused on the gut microbiota's role in systemic diseases, the oral microbiome represents the second largest community of microorganisms, making it a new promising therapeutic target. Periodontitis and dental caries are considered the two main consequences of oral bacterial imbalance. Studies have shown that oral dysbiosis effects are not limited locally. Due to technological advancement, research identified oral bacterial species in heart valves. This evidence links oral dysbiosis with the development of valvular heart disease (VHD). This review focuses on describing the mechanism behind prolonged local inflammation and dysbiosis, that can induce bacteriemia by direct or immune-mediated mechanisms and finally VHD. Additionally, we highlight emerging therapies based on controlling oral dysbiosis, periodontal disease, and inflammation with immunological and systemic effects, that exert beneficial effects in VHD management.

Toxic Effect of Anionic Surfactants on Freshwater Sponge Lubomirskia baikalensis and Its Endosymbiotic Microalgae Chlorella sp.

A number of reports on sponge diseases, including from Lake Baikal, have increased dramatically all over the world in recent years. Herewith, there are various hypotheses for sponge mortality. Lubomirskia baikalensis (phylum Porifera, order Spongillida) is a unique endemic freshwater sponge of Lake Baikal that contains a complex community of eukaryotic and prokaryotic endosymbiotic microorganisms. In this work, we present the first results for the effect of anionic surfactants viz. linear alkylbenzene sulphonates (LAS) at low 10 and 20 µg L−1 concentrations on Baikal sponge species and their symbiotic community as an experimental model. A new toxicity test protocol under conditions close to natural is proposed. It uses the sponge amoebocytes called as SA1-cells, which contain eukaryotic green microalgae Chlorella sp. These SA1-cells are shown to be representative indicator in assessing the impact of anionic surfactants. The acute toxic effect resulted in 97–100% sponge cell death in less than 48 h, as well as 100% symbiotic microalgae Chlorella sp. death over 72 h was noted under LAS solution (20 μg L−1) exposure during in vivo experiments. This includes the cell membrane fatty acid changes, change in the cell sizes, cell swelling, and lysis. Long term exposure to LAS solution (10 μg L−1) reflected in cellular stress (oxidative stress) and accompanied by malondialdehyde formation (0.16–2.0 μg g−1 of dry weight) during 14-day exposure was noted. Oxidative stress and mortality of L. baikalensis are associated with their low antioxidant activity. Trolox-equivalent antioxidant capacity (TEAC) found in the range from 0.00031 to 0.00077 Trolox equivalents for these freshwater sponges.

Mitigation and use of biofilms in space for the benefit of human space exploration

Biofilms are self-organized communities of microorganisms that are encased in an extracellular polymeric matrix and often found attached to surfaces. Biofilms are widely present on Earth, often found in diverse and sometimes extreme environments. These microbial communities have been described as recalcitrant or protective when facing adversity and environmental exposures. On the International Space Station, biofilms were found in human-inhabited environments on a multitude of hardware surfaces. Moreover, studies have identified phenotypic and genetic changes in the microorganisms under microgravity conditions including changes in microbe surface colonization and pathogenicity traits. Lack of consistent research in microgravity-grown biofilms can lead to deficient understanding of altered microbial behavior in space. This could subsequently create problems in engineered systems or negatively impact human health on crewed spaceflights. It is especially relevant to long-term and remote space missions that will lack resupply and service. Conversely, biofilms are also known to benefit plant growth and are essential for human health (i.e., gut microbiome). Eventually, biofilms may be used to supply metabolic pathways that produce organic and inorganic components useful to sustaining life on celestial bodies beyond Earth. This article will explore what is currently known about biofilms in space and will identify gaps in the aerospace industry's knowledge that should be filled in order to mitigate or to leverage biofilms to the advantage of spaceflight.

Analysis of bacterial diversity and functional differences of Jiang-flavored Daqu produced in different seasons.

High-temperature Daqu is an important saccharifying fermenting starter for brewing Jiang-flavored Baijiu. This paper analyzed the diversity characteristics of bacterial communities of Jiang-flavored Daqu (JFDQ) with seasonal changes through Illumina HiSeq sequencing and multivariate statistical methods. Results showed that 21 phyla, 529 genera, and 47 core bacterial genera were identified from the 48 composite samples. Among them, eight functional genera were only found in the summer-produced Daqu (Propionigenium, etc.). Pantoea, Bacillus, Lentibacillus, and Oceanobacillus, respectively, served as the representative functional bacterial genera of the four seasons. Functional prediction analysis showed that Amino acid metabolism Carbohydrate metabolism, Lipid metabolism, Metabolism of cofactors and vitamins, and Nucleotide metabolism (relative abundance > 1%) were the most critical microbial functions in JFDQ, and these key enzymes involved in acetoin biosynthesis, and acetyl-CoA biosynthesis were more abundant in the summer than in the winter. The functional microorganisms community in this paper would provide valuable suggestions about the seasonal production of JFDQ, guiding the Baijiu brewing processes.

Microbiome, immune system and cancer: three sides of the one medal

Purpose of the study to analyze current ideas about the relationship between the microbiota (microbiome) and the human body in the aspect of cancer pathogenesis, ambivalent character of these interactions, and the role of the immune system and immunoinfammatory status that promotes carcinogenesis or prevents neoplastic processes.Material and Methods. Literature search was carried out using Medline, Cochrane Library, Elibrary and PubMed systems, including publications over the last 7 years.Results. The microbiota includes all communities of commensal, symbiotic, and pathogenic microorganisms: bacteria, fungi, archaea, and viruses that colonize the gastrointestinal tract and other organs and tissues. The microbiome is an important factor in cancer pathogenesis due to its involvement in the basic physiological functions of the host, such as digestion, development of the immune system, and modulation of endocrine functions. In the review, the influence of microbiota of different locations (gastrointestinal tract, breast, intravaginal tract) on the development and progression of breast, colorectal and cervical cancers was discussed. The role of the microbiome in cancer pathogenesis is realized by the participation in neoplastic transformation of the epithelium, regulation of tumor progression under conditions of manifested malignant process, and modifcation of the therapeutic effect of standard drugs, including the development of original probiotic-based anticancer agents. The study of the mechanisms of action of the microbiome in the host organism opens up prospects for the development of new approaches to cancer therapy. Particular attention was paid to the mechanisms of the immunomodulatory effect of the microbiota in terms of reducing the risk of malignancy, regulating tumor progression and participating in antitumor therapy. The clinical significance of determining pathogenetically significant microbial markers associated with the aggressive form of cancer, response to treatment and toxicity of therapy was discussed. Particular attention should be paid to the potential mechanisms of interaction between cancer – microbiome – probiotics, since the latter can provide modification of malignancy processes, exert an antitumor effect, and modulate the effectiveness of drug therapy. The feasibility of editing the microbiota by probiotics was considered, and antitumor properties (effects) of bacteria and strategies for modifying the microbiome for the prevention and treatment of cancer were discussed.

Efficiency of food waste as fuel source in Microbial Fuel Cell: A review

This review article discussed about the food waste as a source of bioelectrical energy. Every year the global energy demand increases. While petroleum products currently supply much of this demand, the increasing difficulty of sustained supply and the associated problems of pollution and global warming creates unbalanced energy management and require power sources that are able to sustain for longer periods. Renewable energy generation and waste disposal are two key challenges for the sustainability of future societies. Microbial fuel cells (MFCs) as an alternative renewable technology can run in solid phase and capture bioelectricity from food waste. Food waste being readily available is found to be the potential source for bioelectricity production by optimizing several important factors are optimized, such as the type, number and quality of electrodes, type and amount of substrate, microorganism community, system configuration, and different parameters which increases the amount of electricity generated. Solid microbial fuel cells (SMFCs) were reported to produce relatively small amounts of energy compared with other substrates, but SMFCs are still promising to achieve energy requirement of the future. So this review demonstrates the works of different scientist who potentially produced bioelectricity and looking further for improvements.

Differences in Mycorrhizal Status Induced by Long-Term Fertilization in Roots of Perennial Grassland Species

Abstract Perennial species in a mountain grassland where there is high oligotrophy need support for good development. Soil nutrients, either in large amounts or in small quantities, are the driving force in the management of communities of microorganisms that compete and proliferate nutritionally. The symbiosis between vascular plants and fungi in the soil is extraordinary support for perennial species. The roots of the two dominant species in the meadow were harvested after the moment of flowering. They were prepared and stained according to standard methods for evaluating the colonization process. And the process was quantified with the MycoPatt tool. For both species, differentiated fertilization induces similar changes in fungal strategy. But at the level of the formation of the specific structures of the fungi as well as in their development in the cells of the host plants the differences are visible. Maps exported from the MycoPatt tool can be analysed based on strategies or punctually based on color distribution. One can analyse the distribution of each colour (hyphae-blue, arbuscules-red, vesicles-green) as well as the white areas that are represented by parts of the root where the plant does not allow the development of fungi. The use of the MycoPatt tool simplifies the understanding of the symbiotic process and in addition to the multitude of exported indices, it also provides colonization maps that easily show the changes induced by fertilization on the host plants. Thus, being able to predict the best management practice of the whole ecosystem, to sustainably develop grasslands.

Polifenoli kao nova klasa prebiotika za manipulaciju crevne mikrobiote

A thriving community of microorganisms resides in our intestines, forming complex interactions and producing signaling molecules that can affect human physiological processes. Intrinsic and environmental factors modulate the composition of the microbial ecosystem, with diet representing a key factor affecting the formation of gut microbiota. The epidemic of noncommunicable chronic diseases has been associated with the Western diet, which may modulate the gut microbiota, resulting in a detrimental derangement in the microbial community, termed dysbiosis. Dysbiosis may be reverted through dietary interventions and the application of probiotics and prebiotics. Phenolic compounds represent plant-based nutraceuticals, which can be separated into phenolic acids and polyphenols, that exert prebiotic-like effects and may prevent the development of diseases. Besides direct health-promoting activities, beneficial effects of phenolic compounds may be exerted through their interaction with the gut microbiota. A bidirectional relationship between the gut microbiota and phenolic compounds has been observed, as microorganisms are involved in the metabolism of phenolic compounds, whereas phenolic compounds may affect the composition of the microbiota, with selective stimulatory or inhibitory activity towards the growth of microbial members. In this review, insight into the gut microbiota-polyphenols relationship will be given, with a focus on the application of polyphenols for modifying microbiota and promoting health.

P. aeruginosa interactions with other microbes in biofilms during co-infection.

This review addresses the topic of biofilms, including their development and the interaction between different counterparts. There is evidence that various diseases, such as cystic fibrosis, otitis media, diabetic foot wound infections, and certain cancers, are promoted and aggravated by the presence of polymicrobial biofilms. Biofilms are composed by heterogeneous communities of microorganisms protected by a matrix of polysaccharides. The different types of interactions between microorganisms gives rise to an increased resistance to antimicrobials and to the host's defense mechanisms, with the consequent worsening of disease symptoms. Therefore, infections caused by polymicrobial biofilms affecting different human organs and systems will be discussed, as well as the role of the interactions between the gram-negative bacteria Pseudomonas aeruginosa, which is at the base of major polymicrobial infections, and other bacteria, fungi, and viruses in the establishment of human infections and diseases. Considering that polymicrobial biofilms are key to bacterial pathogenicity, it is fundamental to evaluate which microbes are involved in a certain disease to convey an appropriate and efficacious antimicrobial therapy.

Halophilic Bacteria as a Promising Basis of Biopreparations for Improving the Growth of Autochthonous Strains-Destructors in Salinization Conditions

In some cases, pollution of ecosystems with persistent toxic organic compounds, including polycyclic aromatic hydrocarbons (PAHs), is accompanied by salinization, which significantly inhibits the degradation of these compounds by autochthonous communities of microorganisms. Therefore, new methods of reclamation of such polluted territories are being sought and developed. One of the approaches can be the introduction of bacteria that stimulate the physiological activity of autochthonous destructors. In the course of the conducted study, the moderately halophilic strain Halomonas sp. SMB31 was identified as the most competitive for the intermediates of the destruction of naphthalene (model compound PAH), and its effect on the growth of the halotolerant destructor strain Rhodococcus sp. SMB38 has been evaluated during the degradation of naphthalene under conditions of high salinity (7% NaCl). It is shown that the joint cultivation of Rhodococcus sp. SMB38 and Halomonas sp. SMB31 led to a significant reduction in the duration of the period of adaptation to environmental conditions and an increase in the specific growth rate of the destructor strain. Thus, the obtained results showed the prospects of the studied moderately halophilic strain Halomonas sp. SMB31 for use as a biological preparation for the purpose of activating the physiological processes of autochthonous microorganisms-destructors under conditions of salinization of the environment.

Місце антибактеріальної топічної терапії в дерматології

The cutaneous flora is relatively simple compared to the diverse community of microorganisms that inhabits the mouth, digestive tract and vagina. The ecology of particular areas of the skin is determined by the availability of moisture, the level of sebaceous lipids. Microbial agents, especially Staphilococcus aureus, colonize over 90% of atopic dermatitis skin lesions. Presented our approach to topical treatment of skin diseases with superficial pyoderma, chronical diseases of skin with microbial disbalance by the ointment Ilon Classic.