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Currently, Apis mellifera, commonly known as honeybees, are dying at alarming rates. Beekeepers across the United States lost 45.5% of their managed honeybee colonies from April 2020 to April 2021. This turnover rate is staggeringly high and has been growing. This loss poses a food security and economic problem. Recent studies have shown that diet and the microbes living in honeybee guts are a critical part of this picture. These microbes influence weight gain, energy metabolism, nutrient uptake, development, and immune function. Research shows that higher agricultural intensity decreases the diversity of microbial communities in the nectar of crops. In this thesis, we connect these findings by exploring how agricultural intensification impacts the diversity of the honeybee gut microbiome. To perform this research, live honeybees were collected from both organic and conventional almond farms. The honeybee’s crop stomach and intestine were isolated and the bacterial DNA present was sequenced. These results show that conventional farming practices significantly lower the diversity of the microbiome of honeybees' guts, particularly in the intestinal tract. Given the critical role of intestinal microbes in honeybee health, the reduced microbial diversity caused by agricultural disturbance could be a contributing factor to honeybee decline. With this information, farmers can make better informed choices about their practices and researchers can continue to pursue microbial solutions to honeybee decline.

Western Ghats are designated as world heritage sites and global biodiversity hotspots. Microbial diversity in this forest area has been largely neglected and is getting attention since the end of the last millennium. In this review, we have studied and organized various microorganisms from Western Ghats and their diversity, important characteristics and potential biotechnological applications. Microorganisms from Western Ghats have been explored individually for potential bioactive molecules. While most of the microorganisms were analyzed for antimicrobial activities, there have been studies on microbial promotion of plant growth. The microbes analyzed included from aquatics, soil, rhizosphere, phyllosphere and even as endophytes. There have been microorganisms which have shown antioxidant and anti-cancerous activities. There are microorganisms capable of degrading plant wastes and also xenobiotics. Microorganisms capable of producing industrially important enzymes have also been reported. The present review explores largely neglected microbial diversity with respect to their ability to produce potential bioactive biomolecules.

The aim of this study was to investigate the biological inhibiting effect of a beef-derived Latilactobacillus sakei (RS-25) on the spoilage of beef steaks in overwrapped packaging during the 12 days of storage at 4°C. Beef quality as well as microbial indicators were determined at different intervals during the storage after the inoculation of RS-25 at the 6 log CFU/g, and the high-throughput sequencing was applied to investigate the changes of microbial community structure during the storage. The inoculation of RS-25 on beef had no effect (p > .05) on pH, TBARS, and TVB-N during storage indicating the weak effect of such strain on the eat quality. Furthermore, the rise of L* and the delayed decline of a* and b* reveal the protection effect of RS-25 on the meat color. RS-25 reduced the re-contaminated Salmonella typhimurium by 1.16 log CFU/g (p

Cervical length; Microbial diversity; Pessary Longitud cervical; Diversidad microbiana; Pesario Longitud cervical; Diversitat microbiana; Pessari Introduction Our objective was to compare the vaginal microbiome in low-risk and high-risk pregnant women and to explore a potential association between vaginal microbiome and preterm birth. Material and methods A pilot, consecutive, longitudinal, multicenter study was conducted in pregnant women at 18–22 weeks of gestation. Participants were assigned to one of three groups: control (normal cervix), pessary (cervical length ≤25 mm) and cerclage (cervical length ≤25 mm or history of preterm birth). Analysis and comparison of vaginal microbiota as a primary outcome was performed at inclusion and at 30 weeks of gestation, along with a follow-up of pregnancy and perinatal outcomes. We assessed the vaginal microbiome of pregnant women presenting a short cervix with that of pregnant women having a normal cervix, and compared the vaginal microbiome of women with a short cervix before and after placement of a cervical pessary or a cervical cerclage. Results The microbiome of our control cohort was dominated by Lactobacillus crispatus and inners. Five community state types were identified and microbiome diversity did not change significantly over 10 weeks in controls. On the other hand, a short cervix was associated with a lower microbial load and higher microbial richness, and was not correlated with Lactobacillus relative abundance. After intervention, the cerclage group (n = 19) had a significant increase in microbial richness and a shift towards community state types driven by various bacterial species, including Lactobacillus mulieris, unidentified Bifidobacterium or Enterococcus. These changes were not significantly observed in the pessary (n = 26) and control (n = 35) groups. The cerclage group had more threatened preterm labor episodes and poorer outcomes than the control and pessary groups. Conclusions These findings indicate that a short cervix is associated with an altered vaginal microbiome community structure. The use of a cerclage for preterm birth prevention, as compared with a pessary, was associated with a microbial community harboring a relatively low abundance of Lactobacillus, with more threatened preterm labor episodes, and with poorer clinical outcomes. This study was supported by the Instituto de Salud Carlos III/FEDER FIS PI15/02043; Beca Dexeus Mujer 2015. Francisca Yáñez was supported by a grant from ANID, BECAS Chile, N° 72190278. Zixuan Xie received a fellowship from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Action, Innovative Training Network: FunHoMic; grant number 812969.

Mother vaginal microbes contribute to microbiome of vaginally delivered neonates. Child microbiome can be associated with autoimmune diseases, such as type 1 diabetes (T1D). We collected vaginal DNA samples from 25 mothers with a vaginally delivered child diagnosed with T1D and samples from 24 control mothers who had vaginally delivered a healthy child and analyzed bacteriome and mycobiome of the samples. The total DNA of the samples was extracted, and ribosomal DNA regions (16S for bacteria, ITS2 for fungi) were amplified, followed by next-generation sequencing and machine learning. We found that alpha-diversity of bacteriome was increased (P P P = 0.001). Random forest models were able to effectively predict diabetes and control status of unknown samples (bacteria: 0.86 AUC, fungi: 0.96 AUC). Our data indicate several fungal genera and bacterial metabolic pathways of mother vaginal microbiome to be associated with child T1D. We suggest that early onset of T1D in a child has a relationship with altered mother vaginal microbiome and that both bacteriome and mycobiome contribute to this shift.

Plants and their derivatives, such as fruits, can be inhabited by different bacteria. However, this microbiota is still poorly studied. Among the wide variety of metabolites that bacteria produce, biosurfactants have been identified as potential molecules in the development of bioprocesses for various industrial sectors. In this work, we analyzed and compared the microbiota of fruit residues (mango and orange), in order to compare two possible sources of bioprospecting. For this, a bioinformatics approach was used to perform the taxonomic analysis and the prediction of the functional profile of the microbiota present in the samples. The results showed that the microbiota present in both fruit residues have the potential in biotechnological applications to produce biosurfactants, as these microbiota have genes related to the biosynthesis of these compounds. The common core of the microbiota present in the samples—Stenotrophomonas, Klebsiella, Serratia and Citrobacter—proved, according to the literature, to be composed of biosurfactant producers, showing the biosurfactant potential of the bacteria isolated from orange and mango residues.

Prosthetic valve endocarditis (PVE) remains a serious condition with a high mortality rate. Precise identification of the PVE-associated pathogen/s and their virulence is essential for successful therapy and patient survival. The commonly described PVE-associated pathogens are staphylococci, streptococci, and enterococci, with Staphylococcus aureus being the most frequently diagnosed species. Furthermore, multi-drug resistance pathogens are increasing in prevalence and continue to pose new challenges mandating a personalized approach. Blood cultures in combination with echocardiography are the most common methods to diagnose PVE, often being the only indication, it exists. In many cases, the diagnostic strategy recommended in the clinical guidelines does not identify the precise microbial agent, and frequently, false-negative blood cultures are reported. Despite the fact that blood culture findings are not always a good indicator of the actual PVE agent in the valve tissue, only a minority of re-operated prostheses are subjected to microbiological diagnostic evaluation. In this review, we focus on the diversity and the complete spectrum of PVE-associated bacterial, fungal, and viral pathogens in blood and prosthetic heart valve, their possible virulence potential, and their challenges in making a microbial diagnosis. We are curious to understand if the unacceptable high mortality of PVE is associated with the high number of negative microbial findings in connection with a possible PVE. Herein, we discuss the possibilities and limits of the diagnostic methods conventionally used and make recommendations for enhanced pathogen identification. We also show possible virulence factors of the most common PVE-associated pathogens and their clinical effects. Based on blood culture, molecular biological diagnostics, and specific valve examination, better derivations for the antibiotic therapy as well as possible preventive intervention can be established in the future.

Microbial communities often harbor overwhelming species and gene diversity, making it challenging to determine the important units to study this diversity. We argue that the reduced, and thus tractable, microbial diversity of manmade salterns provides an ideal system to advance this cornerstone issue. We review recent time-series genomic and metagenomic studies of the saltern-dominating bacterial and archaeal taxa to show that these taxa form persistent, sequence-discrete, species-like populations. While these populations harbor extensive intra-population gene diversity, even within a single saltern site, only a small minority of these genes appear to be functionally important during environmental perturbations. We outline an approach to detect and track such populations and their ecologically important genes that should be broadly applicable., This work was partly funded by the US National Science Foundation, awards #1831582 and #1759831 (to KTK), and by the projects CLG2015_66686-C3-1-P, PGC2018-096956-B-C41 and RTC-2017-6405-1 of the Spanish Ministry of Science, Innovation and Universities (to RRM), which were also supported with European Regional Development Fund (FEDER) funds. RRM acknowledges the financial support of the sabbatical stay at Georgia Tech by the grant PRX18/00048 also from the Spanish Ministry of Science, Innovation and Universities.

Streams draining proglacial floodplains harbor benthic biofilms comprised of diverse microbial communities. These high-mountain ecosystems are rapidly changing with climate warming, and it is therefore critical to better understand the mechanisms underlying the assembly of their microbial communities., In proglacial floodplains, glacier recession promotes biogeochemical and ecological gradients across relatively small spatial scales. The resulting environmental heterogeneity induces remarkable microbial biodiversity among proglacial stream biofilms. Yet the relative importance of environmental constraints in forming biofilm communities remains largely unknown. Extreme environmental conditions in proglacial streams may lead to the homogenizing selection of biofilm-forming microorganisms. However, environmental differences between proglacial streams may impose different selective forces, resulting in nested, spatially structured assembly processes. Here, we investigated bacterial community assembly processes by unraveling ecologically successful phylogenetic clades in two stream types (glacier-fed mainstems and non-glacier-fed tributaries) draining three proglacial floodplains in the Swiss Alps. Clades with low phylogenetic turnover rates were present in all stream types, including Gammaproteobacteria and Alphaproteobacteria, while the other clades were specific to one stream type. These clades constituted up to 34.8% and 31.1% of the community diversity and up to 61.3% and 50.9% of the relative abundances in mainstems and tributaries, respectively, highlighting their importance and success in these communities. Furthermore, the proportion of bacteria under homogeneous selection was inversely related to the abundance of photoautotrophs, and these clades may therefore decrease in abundance with the future "greening" of proglacial habitats. Finally, we found little effect of physical distance from the glacier on clades under selection in glacier-fed streams, probably due to the high hydrological connectivity of our study reaches. Overall, these findings shed new light on the mechanisms of microbial biofilm assembly in proglacial streams and help us to predict their future in a rapidly changing environment.IMPORTANCE Streams draining proglacial floodplains harbor benthic biofilms comprised of diverse microbial communities. These high-mountain ecosystems are rapidly changing with climate warming, and it is therefore critical to better understand the mechanisms underlying the assembly of their microbial communities. We found that homogeneous selection dominates the structuring of bacterial communities in benthic biofilms in both glacier-fed mainstems and nonglacier tributary streams within three proglacial floodplains in the Swiss Alps. However, differences between glacier-fed and tributary ecosystems may impose differential selective forces. Here, we uncovered nested, spatially structured assembly processes for proglacial floodplain communities. Our analyses additionally provided insights into linkages between aquatic photoautotrophs and the bacterial taxa under homogeneous selection, potentially by providing a labile source of carbon in these otherwise carbon-deprived systems. In the future, we expect a shift in the bacterial communities under homogeneous selection in glacier-fed streams as primary production becomes more important and streams become "greener".

IntroductionPetroleum pollution resulting from spills and leakages in oil refinery areas has been a significant environmental concern for decades. Despite this, the effects of petroleum pollutants on soil microbial communities and their potential for pollutant biodegradation still required further investigation.MethodsIn this study, we collected 75 soil samples from 0 to 5 m depths of 15 soil profiles in an abandoned refinery to analyze the effect of petroleum pollution on soil microbial diversity, community structure, and network co-occurrence patterns.ResultsOur results suggested soil microbial a-diversity decreased under high C10–C40 levels, coupled with significant changes in the community structure of soil profiles. However, soil microbial network complexity increased with petroleum pollution levels, suggesting more complex microbial potential interactions. A module specific for methane and methyl oxidation was also found under high C10–C40 levels of the soil profile, indicating stronger methanotrophic and methylotrophic metabolic activities at the heavily polluted soil profile.DiscussionThe increased network complexity observed may be due to more metabolic pathways and processes, as well as increased microbial interactions during these processes. These findings highlight the importance of considering both microbial diversity and network complexity in assessing the effects of petroleum pollution on soil ecosystems.

The demand for novel and improved medicine from biological sources to cater to the biopharmaceutical sector has increased significantly in recent years. Among the vast and miscellaneous microbial diversity, fungi provide a prolific source of structurally unique and biologically active secondary metabolites. Natural products obtained from fungi have reformed the era of biomedicine, providing effective drugs that have diverse healing potential. In this review, we focus on the isolation, chemical structure, and bioactivity of biomolecules that have been identified and studied for the first time. Further, we also explain in substantial detail that how the vast uninvestigated Emericellopsis and Simplicillium species may serve as a potential treasure trove of chemically diverse compounds.

Chinese rice wine (Huangjiu), a typical representative of traditional fermented foods in China, is distinguished for its unique flavor. Microorganisms play the most important role in the formation of the unique flavor of Huangjiu. The complex flavor components in Huangjiu are closely related to the metabolism of various microorganisms during the traditional brewing. Therefore, understanding the influence of microbiota on the formation of flavor components in Huangjiu is conducive to the production of Huangjiu with high-quality flavor. In recent years, many scholars have conducted a large number of studies on the microbial community and flavor metabolites during the traditional brewing process of Huangjiu, with the help of high-throughput sequencing (HTS) and mass spectrometry-based metabolomics. This review mainly summarized the current study progress of the microbial diversity of fermentation starters (Qu) and brewing process of Huangjiu, and explored the potential relationship between the microbial community and the characteristic flavor formation of Huangjiu. Through the comparative analysis of literatures, we found that Huangjiu has strong regional characteristics due to the differences in raw materials, Qu and traditional brewing techniques. Dynamics of microbial composition during the traditional brewing of Huangjiu in different regions of China are quite different, making Huangjiu in each region have their own flavor characteristics. Therefore, revealing the relationship between brewing microorganisms and flavor characteristics of Huangjiu is helpful to the directional regulation of flavor quality. According to the current research status, it is proposed that in the future, emerging technologies such as multi-omics, artificial intelligence, and machine learning should be applied to further improve the accuracy of the analysis of microbial flora and flavor components in Huangjiu, so as to accurately reveal the relationship between the microbial community and the formation of characteristic flavor of Huangjiu. Afterwards, high-throughput screening of excellent functional strains from the traditional brewing system should be applied to the industrial production of Huangjiu, so as to improve the overall flavor quality and commercial value.

The Tibetan Plateau is known as the “third pole” on Earth, influencing regional and global climates and providing fresh water to billions of people. Climate change and anthropogenic activities are ...

Microbial diversity is essential for the maintenance of the normal structure and function of bioregenerative life support systems (BLSS). As a typical nutrient-deficient environment (NDE), the BLSS does not provide sufficient types of available substrates for microbial communities, and its internal microbial diversity is usually not high due to interspecific competitive exclusion. However, it is reported that microbial diversity is abnormally high in the International Space Station (ISS) after long-term exposure to low-dose ionizing radiation (LDIR). It remains a mystery why LDIR leads to the formation and maintenance of high microbial diversity. In this study, a series of artificial microbial communities have been cultivated in NDE without and with LDIR, respectively. These communities are composed of three common microbial species (Escherichia coli, Bacillus subtilis and Pseudomonas aeruginosa) in the ISS. By comparing and analyzing the differences in the microbial physiological and behavioral response characteristics in the two scenarios, a reasonable hypothesis was put forward to elucidate the formation and maintenance mechanisms of high microbial diversity in NDE with LDIR. Then a set of kinetic models were developed based on this hypothesis, observed phenomena, and experimental data. Finally, these kinetic models were sufficiently validated and the hypothesis was fully confirmed through large-scale digital simulations. Briefly, two fundamental succession mechanisms of the microbial communities are supposed to exist in NDE with LDIR: substrate-based negative feedback regulation (SNFR) and microbial delayed responses. These two decisive succession mechanisms can give rise to asynchronously convergent fluctuations of microbial populations and significantly alleviate the interspecific competitions. Such a species-for-quantity strategy drives the microbial communities to form and maintain species diversity with higher richness and evenness. This study can lay the theoretical foundation and provide new ideas for the construction of advanced BLSS featured with more robust structures and stronger function.

Despite advances in surgical technique and the expanded use of antibiotics, anastomotic leak remains a dreaded complication leading to increased hospital length of stay, morbidity, mortality, and cost. Data continues to grow addressing the importance of a functional and diverse colonic microbiome to ensure adequate healing. Individual pathogens, such as Enterococcus faecalis and Pseudomonas aeruginosa, have been implicated in the pathogenesis of anastomotic leak. Yet how these pathogens proliferate remains unclear. It is possible that decreased microbial diversity promotes a shift to a pathologic phenotype among the remaining microbiota which may lead to anastomotic breakdown. As the microbiome is highly influenced by diet, antibiotic use, the stress of surgery, and opioid use, these factors may be modifiable at various phases of the surgical process. A large amount of data remains unknown about the composition and behavior of the “normal” gut microbiome as compared with an altered community. Therefore, targeting the gut microbiome as a modifiable factor in anastomotic healing may represent a novel strategy for the prevention of anastomotic leak.

Soybean paste was a traditional fermented product in Northeast China, mainly fermented by molds, yeast, Bacillus, and lactic acid bacteria. This study investigated the dynamic changes of the microbial community and biogenic amine content during the fermentation of the traditional soybean paste. The microbial diversity of soybean paste in different regions was analyzed by MiSeq sequencing technology. The results showed that Penicillium and Tetragenococcus were the dominant microorganisms responsible for the fermentation of soybean paste. Biogenic amine was found in the traditional soybean paste at different fermentation stages, putrescine, and tyramine were the mainly biogenic amines and their content increased with the extension of fermentation time. Serratia in the soybean paste was positively correlated with the formation of spermine, cadaverine (p

The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.

In the quest to find life on other planets, specific extreme terrestrial environments are studied as analogues to present or past conditions on other bodies of our Solar System and beyond. These terrestrial extreme environments often harbour microbial life of high diversity and abundance. These microbes, mostly Bacteria and Archaea, develop survival and adaptation strategies enabling them to withstand harsh conditions. The physico-chemical boundaries for life on Earth are very broad and extreme environments on Earth are highly diversified. Extreme Earth ecosystems bear similarities to past or present environments on planets such as Mars and Venus but may also be analogues to certain moons of gas giants, such as Titan, Europa, and Enceladus. In this review we (1) report the recently described planetary field analogue environment from the Dallol geothermal area in the Danakil Depression, Ethiopia, in which polyextremophilic physical and chemical boundaries for life on Earth coexist; and (2) summarise the physicochemical conditions of extreme terrestrial environments in comparison to extra-terrestrial examples within the framework of our knowledge of microbial life and its adaptation to extremity, suggesting whether and how life could adapt to present or past potential extra-terrestrial habitats. We also explore the distribution and geographical dispersal of microorganisms that inhabit these terrestrial ecosystems and discuss implications for Panspermia.

Rhizosphere microorganisms are the main participants of material transformation and energy cycle in soil. To further explore its composition and variation, the tobacco rhizosphere soil were sequenced by Illumina MiSeq, the microbial community at different growth stages were analyzed and compared. The analysis of Alpha diversity showed that, the Chao1 index, Shannon index of bacteria and Chao1 index of fungi in rhizosphere soil were the highest in tobacco budding stage, while the peak of Shannon index of fungi appeared in tobacco material stage. Principal component analysis (PCA) further showed that at different growth stages, Proteobacteria was the dominant, followed by Actinobacteria, Acidobacteria and Gemmatimonadetes for bacterials; Ascomycota was the dominant, followed by Zygomycota and Basidiomycota for fungi. Under field conditions, the microbial abundance changed with the growth of tobacco, and the microbial diversity reached the peak at budding stage. The bacterial community and abundance between budding and mature stages was highly similar, while the bacterial community in vigorous growth stage is quite different. The similarity of fungal community in budding stage was very low, compared with the other stages; while in other stages was high. This study provides a theoretical basis for further understanding the relationship between tobacco rhizosphere soil microbial diversity and variation, tobacco growth and soil diseases.

International audience; Next-generation sequencing technologies have impressively unlocked capacities to depict the complexity of microbial communities. Microbial community structure is for now routinely monitored by sequencing of 16S rRNA gene, a phylogenetic marker almost conserved among bacteria and archaea. Nevertheless, amplicon sequencing, the most popular used approach, suffers from several biases impacting the picture of microbial communities. Here, we describe an innovative method based on gene capture by hybridization for the targeted enrichment of 16S rDNA biomarker from metagenomic samples. Coupled to near full-length 16S rDNA reconstruction, this approach enables an exhaustive and accurate description of microbial communities by enhancing taxonomic and phylogenetic resolutions. Furthermore, access of captured 16S flanking regions opens link between structure and function in microbial communities.

Plastic debris in the aquatic environment has become a growing concern due to their long-term ecological consequences. Since it is well recognized that plastics provide surfaces for microbial colonization and biofilm formation in the aquatic environment, organic matter cycling can be altered by plastic-associated biofilm due to adhered distinctive microbial functional diversity. Hence, the current study focused on microbial community composition on microplastics (MPs; sizes Also see: https://micro2022.sciencesconf.org/427021/document, In MICRO 2022, Online Atlas Edition: Plastic Pollution from MACRO to nano

A fully anoxic suspended growth process is an appealing alternative to conventional activated sludge (AS) due to considerable aeration reduction and improved carbon processing efficiency for biological nutrient removal (BNR). With development of the hybrid membrane aerated biofilm reactor (MABR) technology, implementation of a fully anoxic suspended growth community in BNR facilities became practical. To better understand potential limitations with the elimination of aeration, we carried out microscopic examination and 16S rRNA gene-based microbial community profiling to determine how an anoxic suspended growth would differ from the conventional aerobic process in floc characteristics, microbial diversity, microbial temporal dynamics, and community assembly pattern. Fewer filamentous populations were found in the anoxic mixed liquor, suggesting easily sheared flocs. The anoxic microbial community had distinct composition and structure, but its diversity and temporal dynamics were similar to the conventional aerobic community. A variety of well-studied functional guilds were also identified in the anoxic community. The anoxic microbial community assembly was more stochastic than the conventional aerobic community, but deterministic assembly was still significant with a large core microbiome adapted to the anoxic condition. A fully anoxic suspended growth process is an appealing alternative to conventional activated sludge (AS) due to considerable aeration reduction and improved carbon processing efficiency for biological nutrient removal (BNR). With development of the hybrid membrane aerated biofilm reactor (MABR) technology, implementation of a fully anoxic suspended growth community in BNR facilities became practical. To better understand potential limitations with the elimination of aeration, we carried out microscopic examination and 16S rRNA gene-based microbial community profiling to determine how an anoxic suspended growth would differ from the conventional aerobic process in floc characteristics, microbial diversity, microbial temporal dynamics, and community assembly pattern. Fewer filamentous populations were found in the anoxic mixed liquor, suggesting easily sheared flocs. The anoxic microbial community had distinct composition and structure, but its diversity and temporal dynamics were similar to the conventional aerobic community. A variety of well-studied functional guilds were also identified in the anoxic community. The anoxic microbial community assembly was more stochastic than the conventional aerobic community, but deterministic assembly was still significant with a large core microbiome adapted to the anoxic condition. Practitioner Points: Flocs developed under the anoxic conditions had less filamentous backbones, implying reduced flocculation capacity and easily sheared flocs. Knowledge about the ecophysiology of Thauera, Thiothrix, and Trichococcus can help achieve good properties of the anoxic flocs. A diverse microbial community sustainably adapted to the fully anoxic condition, containing a variety of filaments, denitrifiers, and PAOs. The anoxic microbial community displayed a similar degree of diversity and temporal dynamics compared to the aerobic counterpart. The anoxic community's assembly was more stochastic, so it may be less subject to changes in environmental variables.

It is believed that polar regions are influenced by global warming more significantly, and because polar regions are less affected by human activities, they have certain reference values for future predictions. This study aimed to investigate the effects of climate warming on soil microbial communities in lake areas, taking Kitezh Lake, Antarctica as the research area. Below-peak soil, intertidal soil, and sediment were taken at the sampling sites, and we hypothesized that the diversity and composition of the bacterial and archaeal communities were different among the three sampling sites. Through 16S rDNA sequencing and analysis, bacteria and archaea with high abundance were obtained. Based on canonical correspondence analysis and redundancy analysis, pH and phosphate had a great influence on the bacterial community whereas pH and nitrite had a great influence on the archaeal community. Weighted gene coexpression network analysis was used to find the hub bacteria and archaea related to geochemical factors. The results showed that in addition to pH, phosphate, and nitrite, moisture content, ammonium, nitrate, and total carbon content also play important roles in microbial diversity and structure at different sites by changing the abundance of some key microbiota.

The dysregulation of skin microflora in patients with atopic dermatitis (AD) has become a research hotspot in recent years. Metagenomic studies have shown that microbial diversity is decreased, whereas the Staphylococcus aureus infection is increased in AD. Keratinocytes are the primary barrier against the invasion of external pathogenic microorganisms. Staphylococcus aureus infection can abnormally activate innate and adaptive immune responses in keratinocytes, resulting in a vicious cycle between Staphylococcus aureus infection and AD. This article reviews the mechanisms of inflammatory damage of keratinocytes induced by Staphylococcus aureus infection in patients with AD, providing a theoretical basis for the study of new targeted drugs. This review also suggests for the management of Staphylococcus aureus infection in patients with AD.

Aging induces significant shifts in the composition of gut microbiota associated with decreased microbial diversity. Age-related changes in gut microbiota include a loss of commensals and an increase in disease-associated pathobionts. These alterations are accelerated by lifestyle factors, such as poor nutritional habits, physical inactivity, and medications. Given that diet is one of the main drivers shaping the gut microbiota, nutritional interventions for restoring gut homeostasis are of great importance to the overall health of older adults. Polyphenols, ubiquitously present in fruits and vegetables, have emerged as promising anti-aging candidates because of their ability to modulate some of the common denominators of aging, including gut dysbiosis. These compounds can influence the composition of the gut microbiota, and gut bacteria metabolize polyphenols into bioactive compounds that produce relevant health effects. Although the role of polyphenols on the aging gut has not been fully characterized, accumulating evidence suggests that these compounds exert selective effects on the gut microbial community. Here, we discuss the reciprocal interactions between polyphenols and gut microbiota and summarize the latest findings on the effects of polyphenols on modulating intestinal bacteria during aging.

Fecal microbiota transplantation (FMT) is a highly effective therapeutic procedure for treating recurrent Clostridium difficile infection. However, the effectiveness of the FMT for the treatment of other chronic diseases associated with intestinal dysbiosis, until recently, remained very low and very variable. A number of studies conducted in recent years have suggested that the success of the FMT is largely dependent on the microbial diversity and composition of the donor stool, which has led to the concept of the existence of FMT superdonors, which are considered individuals whose FMT is accompanied by a high efficiency. The review presents some of the results of the FMT with the involvement of superdonors, describes the possible mechanisms and factors affecting the success of the FMT. It is concluded that the high diversity of the gut microbiota, especially in the donor, seems to be the best predictor of the patient’s response to the FMT. It is assumed that the identification and subsequent characterization of superdonor intestinal microbiomes will improve our understanding of the microbial component of chronic diseases and will allow the use of the FMT in a more targeted manner in the future.

Smoked, and especially smokeless, tobacco are major causes of oral cancer globally. Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing. Oral swab samples were collected from smokers, smokeless tobacco users, and healthy controls (n = 44). Microbial DNA was extracted and the 16S rRNA gene profiled using the Illumina MiSeq platform. Sequencing reads were processed using DADA2, and taxonomical classification was performed using the phylogenetic placement method. Differentially abundant taxa were identified using DESeq2, while functional metagenomes based on KEGG orthology abundance were inferred using LIMMA. A significantly higher microbial diversity was observed in smokeless tobacco users and smokers relative to controls (P 1.5; BH adj P

Plant-associated microbiomes assist their host in a variety of activities, spanning from nutrition to defence against herbivores and diseases. Previous research showed that plant-associated microbiomes shift their composition when plants are exposed to stressors, including herbivory. However, existing studies explored only single herbivore-plant combinations, whereas plants are often attacked by several different herbivores, but the effects of multiple herbivore types on the plant microbiome remain to be determined. Here, we first tested whether feeding by different herbivores (aphids, nematodes and slugs) produces a shift in the rhizosphere bacterial microbiota associated with potato plants. Then, we expanded this question asking whether the identity of the herbivore produces different effects on the rhizosphere microbial community. While we found shifts in microbial diversity and structure due to herbivory, we observed that the herbivore identity does not influence the diversity or community structure of bacteria thriving in the rhizosphere. However, a deeper analysis revealed that the herbivores differentially affected the structure of the network of microbial co-occurrences. Our results have the potential to increase our ability to predict how plant microbiomes assemble and aid our understanding of the role of plant microbiome in plant responses to biotic stress.

Preventive vaccination is currently the most affordable and economical way to reduce morbidity and mortality from many infections, improve quality and human life expectancy with an almost ideal balance of benefits and risks among all medical procedures. The article deals with the reasons for variability of the immune response caused by vaccines, between individuals and between populations, which is of fundamental importance for human health. The authors have presented data indicating a key role of the gut microbiota in the control of the immune response to vaccination. Particular attention is paid to the microbial diversity in different loci of the body. The role of microorganisms in the proper functioning of the body and the formation of a number of pathological conditions is described. Most modern vaccines are live-attenuated, killed / inactivated or subunit (recombinant) vaccines, and they are designed for the parenteral route of administration. Most of these vaccines elicit a weak immune response, especially in the mucous membranes, due to the route of administration and are associated with weak cell-mediated immunity. Therefore, mechanisms that can enhance virus-specific vaccine immunity in infants and children are required, such as the use of more potent or selective immunity-enhancing adjuvants. Some probiotic strains may be considered as promising vaccine adjuvants. This article evaluates the recent clinical studies of probiotics used to enhance vaccine-specific immunity in adults and infants. The present-day knowledge on the role of the probiotic strain Lactobacillus rhamnosus GG with the aim of activating immunity after vaccination are presented.

Fusarium wilt of tomato is widespread throughout China, and the large spread of Fusarium oxysporum f. sp.lycopersici (FOC) in the soil is the main reason. The application of vermicompost provides a...

With the environmental problems brought about by the excessive use of fertilizers and pesticides, numerous biological amendments have been developed and used in recent years. This study, through in-depth analysis of the effects of two different microbial amendments on the microbial diversity in the garlic rhizosphere, provides a theoretical basis and data support for farmers to select microbial amendments. In the experiment, two different microbial amendments were applied to garlic, and its rhizosphere soil was collected after 10, 20, 30, and 40 days. The polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyze bacterial diversity in the garlic rhizosphere soil. The total abundance and diversity of microbial flora in the rhizosphere soil of garlic increased after application of microbial amendments to soil or plants. Plant growth was significantly better in the soil treatment than the plant treatment and the water control. The two dominant bacteria of uncultured gamma proteobacterium and Uncultured Gemmatimonadete existed only in the soil treatment. After 40 day of treatment, the abundance in the rhizosphere soil of these four bacterial strains (Uncultured Bacillus sp. clone D.an-22, Mesorhizobium sp., uncultured gamma proteobacterium, and Pseudomonas boreopolis) was greater in the soil than the plant treatment and the control. The irrigation of microbial amendments not only influenced the structure and abundance of rhizosphere microorganisms, and also promoted the colonization by microorganisms. The five bacterial strains of uncultured gamma proteobacterium, Uncultured Gemmatimonadetes, Uncultured Bacillus sp. clone D.an-22, Mesorhizobium sp., Pseudomonas boreopolis could facilitate the growth and enhance resistance of garlic, establishing a foundation for the use of microbial amendments and providing new ideas and methods for environmental management and protection.

Analysis of water bodies, such as rivers and lakes can provide an insight into their intrinsic composition and potential impact on the environment. Water samples collected from four designated sites in Idah River, were assessed for their physicochemical parameters and microbial diversity using standard procedures. The temperature from all sites was 26.00°C and the pH ranged from 6.93 to 7.08. Turbidity values ranged between 32.00 and 38.00 NTU, while dissolved oxygen ranged between 6.28 and 9.28 ppm. Heavy metals, such as Selenium and Arsenic (with peak values of 0.10 and 0.09 ppm, respectively) were detected in the river. However, dissolved oxygen, arsenic and turbidity values across all sites exceeded the maximum limit set by World Health Organisation and the Standard Organisation of Nigeria. The total heterotrophic bacterial counts showed excessive bacterial load from all sample sites, while pathogenic bacteria, including Escherichia coli, Klebsiella and Shigella species, were isolated from regions with intense anthropogenic activities along the river, indicative of microbial pollution. Fungal studies identified the presence of Fusarium, Aspergillus and Trichoderma species as the most abundant in the river. Obtained results showed that Idah River is exposed to heavy metal seepage and subject to microbial contamination. Therefore, continuous monitoring and better management of the river body is recommended to prevent disease outbreak. Key words: Aquatic ecosystems, Idah River, microbial diversity, physicochemical analysis.

Thermal springs have been the most resourceful ecological niches to understand the intricacies of the microbial community structure building. In the present study, the microbial community structure...

The construction of amplified 16S rRNA gene libraries has been a major methodology for bacterial/archaeal environmental community profiling for decades. Over the years, a variety of alternative pri...

BACKGROUND AND OBJECTIVES The skin microbiota partly determined by epidermal barrier plays an important role in acne vulgaris and intense pulsed light (IPL) has been verified as a safe and effective therapeutic option for this disease. Nevertheless, the exact role of the IPL treatment on the skin microbiota and epidermal barrier for patients with acne vulgaris remains unclear. This article was designed to solve this problem. STUDY DESIGN/MATERIALS AND METHODS Nineteen healthy controls and 20 patients with mild to moderate acne were enrolled in this study, who received IPL treatment for 12 weeks. The epidermal barrier and skin samples were collected at baseline and after treatment. The microbial diversity was analyzed based on a high-throughput sequencing approach, which targets the V3-V4 region of the bacteria 16S ribosomal RNA genes. RESULTS After treatment of IPL, the Global Acne Grading System (GAGS) scores, sebum, sclererythrin, and red area of patients were significantly improved by IPL treatment (P

Adding manure to croplands restores carbon and nutrients in depleted soils, while addressing a waste disposal need. This practice depends on the abundance and activity of microbial communities to break down manure inputs, which provide carbon for microbial growth and release nutrients for plant and microbial uptake. In a 2-year field study, we measured changes to soil physicochemical properties and microbial community composition in a conventional rotation of summer sileage corn and winter wheat. Three ratios of manure to mineral N fertilizer were used: all manure (100% of plant N from manure), mixed (50% plant N from by manure and 50% from mineral fertilizer), and all mineral (100% plant N from mineral fertilizer). Yields of corn and wheat were similar across treatments. Soil microbial community dissimilarity increased with higher ratios of application, suggesting a dose-dependent relationship between manure application and microbial community composition. Both microbial biomass and dissolved organic carbon showed the greatest response immediately following manure application, then decreased until the next application. The Shannon index increased shortly after manure application, with the largest increase observed in soils receiving manure input. Many of the taxa that increased in relative abundance following manure application were specifically taxa known to be present in manure and not common or present in soil before manure application. Microbial community changes following manure application were transitory, indicating that without continual inputs of resources, these alterations are not maintained. This was in contrast to microbial biomass which slowly increased in size over the 2-year study period. Better understanding of how manure interacts with microbial communities will help in developing better nutrient management practices and help reduce our reliance on mineral fertilizers.

High-throughput platforms facilitating screening campaigns of environmental samples are needed to discover new products of natural origin counteracting the spreading of antimicrobial resistances constantly threatening human and agricultural health. We applied a combination of droplet microfluidics and fluorescence-activated cell sorting (FACS)-based technologies to access and assess a microbial environmental sample. The cultivation performance of our microfluidics workflow was evaluated in respect to the utilized cultivation media by Illumina amplicon sequencing of a pool of millions of droplets, respectively. This enabled the rational selection of a growth medium supporting the isolation of microbial diversity from soil (five phyla affiliated to 57 genera) including a member of the acidobacterial subgroup 1 (genus Edaphobacter). In a second phase, the entire diversity covered by 1071 cultures was used for an arrayed bioprospecting campaign, resulting in > 6000 extracts tested against human pathogens and agricultural pests. After redundancy curation by using a combinatorial chemical and genomic fingerprinting approach, we assigned the causative agents present in the extracts. Utilizing UHPLC-QTOF-MS/MS-guided fractionation and microplate-based screening assays in combination with molecular networking the production of bioactive ionophorous macrotetrolides, phospholipids, the cyclic lipopetides massetolides E, F, H and serratamolide A and many derivatives thereof was shown.

Crustaceans such as prawn and shrimp are nutritious seafood and contain high level of protein. However, due to high-water activity and neutral pH, crustaceans are highly susceptible to spoilage microorganisms that are present as normal microbiota. Development stages and culture environment, diet composition and storage temperature were highlighted in this review as factors that contribute to the composition of microbial communities present in prawn and shrimp. However, the use of biofloc technology during culturing/farming could help to reduce the microbial load at pre-harvest level while the use of neutralized oxidized water could be used to further reduce microbial load during post-harvest handling of the seafood. The use of both biofloc technology and neutral electrolyzed oxidizing water would therefore help to preserve the quality and shelf-life of prawn and shrimp.

Rhizobacteria have huge potential for biocontrol activity against many plant pathogens. Isolation and identification are therefore crucial to understand their microbial diversity and ecological imp...

To explain the differences in microbial diversity between soil from termite mounds and their nearby soils, we evaluated the impact of termite biopedturbation on the respiration profiles of microorganisms from termite mound soils. The MicroRespTM technique was employed to assess the whole-soils’ community-level-physiological-profiles (CLPP) assays using 21 carbon substrates chosen on the ground of significance to biotas dwellings in the soil. Principal component analyses showed that carbon substrate groups in the soils from termite mound were separated from those of the nearby soils. The results supported our first premise that the CLPP of soils from termite mounds could be distinguishable from the CLPP of the nearby soil and the degree of the differences was based on which substrates were added in the analysis. The assumption that any variance established in the CLPP could be attributed to a higher use of structurally complex carbon substrates in soils from termite mounds compared to the nearby soil samples was also supported. The higher soil respiration and the capacity to degrade carbon sources in soils from termite mounds than the nearby soil samples connote a rise in microbial functional diversity due to the differences in the diversity of microorganisms between both habitats.

The dynamic changes in microbial diversity during the aerobic composting of agricultural crop straw with additives were evaluated using high-throughput sequencing at four phases of composting (mesophilic, thermophilic, cooling and maturation phases). In addition, the physicochemical parameters of the composting system were determined in this study. The fermentation time of the thermophilic period was prolonged with the addition of urea or urea combined with a microbial agent. The ratio of C/N and germination index variation indicated that the additives were favorable for composting, because the additives directly changed the physicochemical properties of the compost and had effects on the diversity and abundance of bacteria and fungi. The abundance of operational taxonomic units (OTUs), diversity index (Shannon) and richness index (Chao1) of fungi and bacteria were found to significantly increase when urea+microbial agents were added to straw in the thermophilic phase. The relative abundance of the predominant bacteria and fungi at the phylum and genus levels differed during different composting phases. The abundance of the phyla Firmicutes and Proteobacteria declined in the order of treatments SNW>SN>S (S is straw only compost; SN is straw+5 kg t−1 urea compost; and SNW is straw+5 kg t−1 urea+ 1 kg t−1 microbial agent compost) in the thermophilic phase. The abundance of the genera Staphylococcus, Bacillus and Thermobifida followed the same order in the mesophilic phase. Ascomycota accounted for more than 92% of the total fungal sequences. With the progression of the composting process, the abundance of Ascomycota decreased gradually. The abundance of Ascomycota followed the order of S>SN>SNW during the thermophilic phase. The abundance of Aspergillus accounted for 4–59% of the total abundance of fungi and increased during the first two sampling periods. Aspergillus abundance followed the order of SNW>SN>S. Additionally, principal component analysis (PCA) revealed that the community compositions in the straw and straw+urea treatments were similar, and that the bacterial communities in treatments S, SN and SNW in the mesophilic phase (at day 1) were different from those observed in three other phases (at days 5, 11, and 19, respectively), while the fungal communities showed only slight variations in their structure in response to changes in the composting process. Canonical correlation analysis (CCA) and redundancy analysis (RDA) showed that total carbon (TC), NO3−-N (NN), electrical conductivity (EC) and pH were highly correlated with community composition. Therefore, this study highlights that the additives are beneficial to straw composting and result in good quality compost.