Environmental Microbiota Research Articles

Rheumatoid arthritis: advances in treatment strategies.

Rheumatoid arthritis (RA) is characterised by severe joint and bone damage due to heightened autoimmune response at the articular sites. Worldwide annual incidence and prevalence rate of RA is 3 cases per 10,000 population and 1%, respectively. Several genetic and environmental (microbiota, smoking, infectious agents) factors contribute to its pathogenesis. Although convention treatment strategies, predominantly Disease Modifying Anti Rheumatic Drugs (DMARDs) and Glucocorticoids (GC), are unchanged as the primary line of treatment; novel strategies consisting of biological DMARDs, are being developed and explored. Personalized approaches using biologicals targetspecific pathways associated with disease progression. However, considering the economic burden and side-effects associated with these, there is an unmet need on strategies for early stratification of the inadequateresponders with cDMARDs. As RA is a complex diseasewith a variable remission rate, it is important not only to evaluate the current status of drugs in clinicalpractice but also those with thepotential ofpersonalisedtherapeutics. Here, we provide comprehensive data on the treatment strategies in RA, including studies exploring various combination strategies in clinical trials. Our systematic analysis of current literature found that conventional DMARDs along with glucocorticoid may be best suited for early RA cases and a combination ofconventional and targetedDMARDs could be effective for treating seronegative patients with moderate to high RA activity. Clinical trials with insufficient responders to Methotrexate suggest that adding biologicals may help in such cases.However,certain adverse events associated with the current therapy advocate exploringnovel therapeutic approaches such as gene therapy, mesenchymal stem cell therapy in future.

Transmission of antibiotic resistance at the wildlife-livestock interface

Antibiotic-resistant microorganisms (ARMs) are widespread in natural environments, animals (wildlife and livestock), and humans, which has reduced our capacity to control life threatening infectious disease. Yet, little is known about their transmission pathways, especially at the wildlife-livestock interface. This study investigated the potential transmission of ARMs and antibiotic resistance genes (ARGs) between cattle and wildlife by comparing gut microbiota and ARG profiles of feral swine (Sus scrofa), coyotes (Canis latrans), cattle (Bos taurus), and environmental microbiota. Unexpectedly, wild animals harbored more abundant ARMs and ARGs compared to grazing cattle. Gut microbiota of cattle was significantly more similar to that of feral swine captured within the cattle grazing area where the home range of both species overlapped substantially. In addition, ARMs against medically important antibiotics were more prevalent in wildlife than grazing cattle, suggesting that wildlife could be a source of ARMs colonization in livestock.

Effects of Habitat River Microbiome on the Symbiotic Microbiota and Multi-Organ Gene Expression of Captive-Bred Chinese Giant Salamander.

The reintroduction of captive-bred individuals is a primary approach to rebuild the wild populations of the Chinese giant salamander (Andrias davidianus), the largest extant amphibian species. However, the complexity of the wild habitat (e.g., diverse microorganisms and potential pathogens) potentially threatens the survival of reintroduced individuals. In this study, fresh (i.e., containing environmental microbiota) or sterilized river sediments (120°C sterilized treatment) were added to the artificial habitats to treat the larvae of the Chinese giant salamander (control group—Cnt: 20 individuals, treatment group 1 with fresh river sediments—T1: 20 individuals, and treatment group 2 with sterilized river sediments—T2: 20 individuals). The main objective of this study was to test whether this procedure could provoke their wild adaptability from the perspective of commensal microbiotas (skin, oral cavity, stomach, and gut) and larvae transcriptomes (skin, spleen, liver, and brain). Our results indicated that the presence of habitat sediments (whether fresh or sterilized) reshaped the oral bacterial community composition. Specifically, Firmicutes decreased dramatically from ~70% to ~20–25% (mainly contributed by Lactobacillaceae), while Proteobacteria increased from ~6% to ~31–36% (mainly contributed by Gammaproteobacteria). Consequently, the proportion of antifungal operational taxonomic units (OTUs) increased, and the function of oral microbiota likely shifted from growth-promoting to pathogen defense. Interestingly, the skin microbiota, rather than the colonization of habitat microbiota, was the major source of the pre-treated oral microbiota. From the host perspective, the transcriptomes of all four organs were changed for treated individuals. Specifically, the proteolysis and apoptosis in the skin were promoted, and the transcription of immune genes was activated in the skin, spleen, and liver. Importantly, more robust immune activation was detected in individuals treated with sterilized sediments. These results suggested that the pathogen defense of captive-bred individuals was improved after being treated, which may benefit their survival in the wild. Taken together, our results suggested that the pre-exposure of captive-bred Chinese giant salamander individuals to habitat sediments could be considered and added into the reintroduction processes to help them better adapt to wild conditions.

Dynamics of Bacterial Composition and Association with Quality Formation and Biogenic Amines Accumulation during Fish Sauce Spontaneous Fermentation.

High-throughput sequencing and high-pressure liquid chromatography (HPLC) methods were used to investigate the influences of microbial dynamics on the quality and biogenic amine (BA) content during fish sauce fermentation. The homogeneity of total viable bacteria and lactic acid bacteria in fish sauce becomes higher as fermentation progresses. Tetragenococcus was the key genus of fish sauce fermentation. Carnobacterium (38.43%) and Lentibacillus (41.01%) were the dominant genera in the samples fermented for 3 months and 18 months, respectively. These three bacterial genera were significantly related to the physicochemical characteristics and characteristic flavors of the sauces. Tetragenococcus was significantly positively correlated with nitrogen oxides, the main characteristic flavor components in fish sauce. The BA content in fish sauce fermentation increased from 106.88 to 376.03 mg/kg, and the content of histamine reached 115.30 mg/kg at the end of fermentation, indicating that fish sauce has health risks. About 66.67% of Lentibacillus isolates were able to produce a large amount of BA, suggesting that Lentibacillus was the key genus for BA accumulation in fish sauce fermentation. Research on reducing the content of BA in fish sauce by intervening with regard to the fermentation temperature showed that a safe fish sauce product could be obtained at the fermentation temperature of about 25°C. These results help us to understand the contribution of microbial community composition to fish sauce fermentation and provide a basis for improving the quality and safety of fermented fish sauce. IMPORTANCE Traditional fermentation of fish sauce is mainly carried out by complex microbial communities from raw anchovies and processing environments. However, it is still unclear how the environmental microbiota influences the quality and the safety of fish sauce products. Therefore, this study comprehensively explained the influence of microorganisms on the quality and safety of fish sauce during the fermentation process in terms of physicochemical characters, flavors, and BA. Additionally, the accumulation of BA in fish sauce fermentation was controlled by intervening in the fermentation temperature. This finding contributes to a deeper understanding of the role of environmental microbiota during fermentation and provides data support for improving the safety of fish sauce.

Paroxetine effects in adult male rat colon: Focus on gut steroidogenesis and microbiota

Paroxetine, a selective serotonin reuptake inhibitor (SSRI), is prescribed to treat psychiatric disorders, although an off-label SSRI use is also for functional gastrointestinal disorders. The mutual correlation between serotonin and peripheral sex steroids has been reported, however little attention to sex steroids synthesized by gut, has been given so far. Indeed, whether SSRIs, may also influence the gut steroid production, immediately after treatment and/or after suspension, is still unclear. The finding that gut possesses steroidogenic capability is of particular relevance, also for the existence of the gut-microbiota-brain axis, where gut microbiota represents a key orchestrator. On this basis, adult male rats were treated daily for two weeks with paroxetine or vehicle and, 24 h after treatment and at 1 month of withdrawal, steroid environment and gut microbiota were evaluated. Results obtained reveal that paroxetine significantly affects steroid levels, only in the colon but not in plasma. In particular, steroid modifications observed immediately after treatment are not overlap with those detected at withdrawal. Additionally, paroxetine treatment and its withdrawal impact gut microbiota populations differently. Altogether, these results suggest a biphasic effect of the drug treatment in the gut both on steroidogenesis and microbiota.

Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle.

Establishment and development of gut microbiota during vertebrates' early life are likely to be important predictors of health and fitness. Host-parental and host-environment interactions are essential to these processes. In oviparous reptiles whose nests represent a source of the parent's microbial inocula, the relative role of host-selection and stochastic environmental factors during gut microbial assemblage remains unknown. We sampled eggs incubated in artificial nests as well as hatchlings and juveniles (up to 30 days old) of the yellow-spotted Amazon river turtle (Podocnemis unifilis) developing in tubs filled with river water. We examined the relative role of the internal egg microbiota and the abiotic environment on hatchling and juvenile turtle's cloacal microbiota assemblages during the first 30 days of development. A mean of 71% of ASVs in hatched eggs could be traced to the nest environmental microbiota and in turn a mean of 77% of hatchlings' cloacal ASVs were traced to hatched eggs. Between day 5 and 20 of juvenile turtle's development, the river water environment plays a key role in the establishment of the gut microbiota (accounting for a mean of 13%-34.6% of cloacal ASVs) and strongly influences shifts in microbial diversity and abundance. After day 20, shifts in gut microbiota composition were mainly driven by host-selection processes. Therefore, colonization by environmental microbiota is key in the initial stages of establishing the host's gut microbiota which is subsequently shaped by host-selection processes. Our study provides a novel quantitative understanding of the host-environment interactions during gut microbial assemblage of oviparous reptiles.

Interaction of Microbiota between Fish and the Environment of an In-Pond Raceway System in a Lake.

Due to its ability to collect and remove aquaculture waste, an in-pond raceway system (IPRS) has been used to decrease the uncontrolled waste discharge in the traditional cage aquaculture method in large water bodies. However, when applied to large water bodies, its environmental performance is still lacking. This study focused on analyzing the microbial characteristics and the interaction between largemouth bass (gill and gut) microbiota and the environment (water and sediment) microbiota of an IPRS. Further, it revealed the primary relationship from the perspective of microbiota in the IPRS. The results show that (1) the alpha diversity of microbiota in the water is significantly lower than that of fish and sediment. The relationship between water microbiota and fish microbiota is limited. (2) The water microbiota inside and outside the tank showed high similarity and were not significantly affected by environmental factors. (3) The SourceTrack analysis showed that fish microbiota is one of the primary sources of sediment microbiota, and more than 15% of the sediment microbiota come from fish. Microbes such as Faecalibacterium, Escherichia-Shigella, and Bacteroides can significantly enrich the sediment. Our study revealed the characteristics and preliminary interaction of fish and environmental microbiota in the IPRS. It provided a reference for evaluating microbial health status in the application of IPRS in large water bodies’ aquaculture.

Study Protocol: Gut microbiota profiles implicated in the onset of autism spectrum disorders in preterm infants: A two-year follow-up study

IntroductionPreterm infants are at high-risk of developing autism spectrum disorders (ASD). The underlying mechanisms that explain the link between prematurity and ASD are unclear. Perinatal environmental factors may disrupt the gut-brain communication, when the gut microbiome composition is established and brain programming occurs. Therefore, the disruption of the gut-brain axis communication in response to perinatal environmental events may shed light on the association between prematurity and ASD.ObjectivesTo describe a new research project protocol which aim is to develop a dynamic model of gut microbiota variation in response to environmental factors that modulate the ASD risk in preterm infants.MethodsA two-year prospective observational study will be carried out, in which preterm infants will be assessed at birth, 40th postmenstrual week, at 6, 12, and 24 months of corrected age. Two-hundred preterm infants will be recruited. A comprehensive assessment will be conducted by collecting data on sociodemographic characteristics, medical history, family functioning, neurodevelopment, ASD screening, and diagnosis. Microbiome composition and microbial activity will be determined from feces.ResultsThe expected results are: i) to characterize ASD since its early manifestations in an at-risk population, allowing an early diagnosis and intervention to improve clinical outcomes; ii) to identify early microbiota biomarkers in order to find potential pathophysiological pathways; iii) to understand the protective and risk factors associated to ASD since perinatal period.ConclusionsA two-year predictive model will be generated based on environmental and gut microbiota variables. This predictive model of ASD would allow prevention, early diagnosis, improvement of prognosis, and personalized treatments in preterm infants.DisclosureNo significant relationships.

Humanization of wildlife gut microbiota in urban environments.

Urbanization is rapidly altering Earth's environments, demanding investigation of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans), crested anole lizards (Anolis cristatellus), and white-crowned sparrows (Zonotrichia leucophrys) acquire gut microbiota constituents found in humans, including gut bacterial lineages associated with urbanization in humans. Comparisons of urban and rural wildlife and human populations revealed significant convergence of gut microbiota among urban populations relative to rural populations. All bacterial lineages overrepresented in urban wildlife relative to rural wildlife and differentially abundant between urban and rural humans were also overrepresented in urban humans relative to rural humans. Remarkably, the bacterial lineage most overrepresented in urban anoles was a Bacteroides sequence variant that was also the most significantly overrepresented in urban human populations. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities.

Clay chips and beads capture in situ barley root microbiota and facilitate in vitro long-term preservation of microbial strains.

Capturing the diverse microbiota from healthy and/or stress resilient plants for further preservation and transfer to unproductive and pathogen overloaded soils, might be a tool to restore disturbed plant–microbe interactions. Here, we introduce Aswan Pink Clay as a low-cost technology for capturing and storing the living root microbiota. Clay chips were incorporated into the growth milieu of barley plants and developed under gnotobiotic conditions, to capture and host the rhizospheric microbiota. Afterward, it was tested by both a culture-independent (16S rRNA gene metabarcoding) and -dependent approach. Both methods revealed no significant differences between roots and adjacent clay chips in regard total abundance and structure of the present microbiota. Clay shaped as beads adequately supported the long-term preservation of viable pure isolates of typical rhizospheric microbes, i.e. Bacillus circulans, Klebsiella oxytoca, Sinorhizobium meliloti, and Saccharomyces sp., up to 11 months stored at −20°C, 4°C, and ambient temperature. The used clay chips and beads have the capacity to capture the root microbiota and to long-term preserve pure isolates. Hence, the developed approach is qualified to build on it a comprehensive strategy to transfer and store complex and living environmental microbiota of rhizosphere toward biotechnological application in sustainable plant production and environmental rehabilitation.

The Stressful Effects of Microplastics Associated With Chromium (VI) on the Microbiota of Daphnia Magna

Contamination by microplastics (particles < 1 mm) is a growing and alarming environmental problem in freshwater systems. Evidence suggests that industrial effluents could be one of the critical point sources of microplastics and other pollutants, and their interaction can cause organismal stress and affect host and environmental microbial communities. We tested the individual and combined effects of microplastics and other pollutants on host survival and host associated (commensal) bacterial diversity. We exposed Daphnia magna to 1 µm microplastic beads with a concentration of approximately 1820 particles/ml and chromium (VI) simultaneously with treatments of 2 and 5 ppm for 72 h. DNA extraction was done to amplify and sequence the ribosomal Bacterial 16S from both the water and the Daphnia. Daphnia experienced low mortality in treatments microplastics (13.3%) and 2 ppm chromium VI (30%) individually. However, the combination of microplastics and 2 ppm chromium (VI) increased the mortality to 74.4%. In the treatments with 5 ppm of chromium (VI) mortality rose to 100% after 30 h of exposure. Microbial diversity changed in response to microplastics, chromium (VI), and both combined exposure. Microplastics and toxic metals can cause dysbiosis of freshwater environmental microbiota, whole host microbiota, and host survival. This work stresses the importance to assess how pollutants’ individual and joint effects could affect organisms including their microbiome.

Enzymatically triggered delignification through a novel stable laccase: A mixed in-silico /in-vitro exploration of a complex environmental microbiota

Laccases have been broadly applied as a multitasking biocatalyst in various industries, but their applications tend to be limited by easy deactivation, lack of adequate stability, and susceptibility under complex conditions. Identifying stable laccase as a green-biocatalyst is crucial for developing cost-effective biorefining processes. In this direction, we attempted in-silico screening a stable metagenome-derived laccase (PersiLac1) from tannery wastewater in a complex environment. The laccase exhibited high thermostability, retaining 53.19% activity after 180 min at 70 °C, and it was stable in a wide range of pH (4.0–9.0). After 33 days of storage at 50°C, pH 6.0, the enzyme retained 71.65% of its activity. Various metal ions, inhibitors, and organic solvents showed that PersiLac1 has a stable structure. The stable PersiLac1 could successfully remove lignin and phenolic from quinoa husk and rice straw. In the separate hydrolysis and fermentation process (SHF) after 72 h, hydrolysis was obtained 100% and 73.4% for quinoa husk and rice straw, and fermentation by the S. cerevisiae was be produced 41.46 g/L and 27.75g/L ethanol, respectively. Results signified that the novel lignin-degrading enzyme was confirmed to have great potential for industrial application as a green-biocatalyst based on enzymatically triggered to delignification and detoxify lignocellulosic biomass.

Insights into the Profile of the Human Expiratory Microbiota and Its Associations with Indoor Microbiotas.

Microorganisms residing in the human respiratory tract can be exhaled, and they constitute a part of environmental microbiotas. However, the expiratory microbiota community and its associations with environmental microbiotas remain poorly understood. Here, expiratory bacteria and fungi and the corresponding microbiotas from the living environments were characterized by DNA amplicon sequencing of residents’ exhaled breath condensate (EBC) and environmental samples collected from 14 residences in Nanjing, China. The microbiotas of EBC samples, with a substantial heterogeneity, were found to be as diverse as those of skin, floor dust, and airborne microbiotas. Model fitting results demonstrated the role of stochastic processes in the assembly of the expiratory microbiota. Using a fast expectation–maximization algorithm, microbial community analysis revealed that expiratory microbiotas were differentially associated with other types of microbiotas in a type-dependent and residence-specific manner. Importantly, the expiratory bacteria showed a composition similarity with airborne bacteria in the bathroom and kitchen environments with an average of 12.60%, while the expiratory fungi showed a 53.99% composition similarity with the floor dust fungi. These differential patterns indicate different relationships between expiratory microbiotas and the airborne microbiotas and floor dust microbiotas. The results here illustrated for the first time the associations between expiratory microbiotas and indoor microbiotas, showing a potential microbial exchange between the respiratory tract and indoor environment. Thus, improved hygiene and ventilation practices can be implemented to optimize the indoor microbial exposome, especially in indoor bathrooms and kitchens.

Domestic Environment and Gut Microbiota: Lessons from Pet Dogs

Accumulating data show the involvement of intestinal microbiota in the development and maintenance of numerous diseases. Many environmental factors influence the composition and function of the gut microbiota. An animal model subjected to the same environmental constraints that will allow better characterization of the microbiota–host dialogue is awaited. The domestic dog has physiological, dietary and pathological characteristics similar to those of humans and shares the domestic environment and lifestyle of its owner. This review exposes how the domestication of dogs has brought them closer to humans based on their intrinsic and extrinsic similarities which were discerned through examining and comparing the current knowledge and data on the intestinal microbiota of humans and canines in the context of several spontaneous pathologies, including inflammatory bowel disease, obesity and diabetes mellitus.

Gut microbiota of ring-tailed lemurs (Lemur catta) vary across natural and captive populations and correlate with environmental microbiota

BackgroundInter-population variation in host-associated microbiota reflects differences in the hosts’ environments, but this characterization is typically based on studies comparing few populations. The diversity of natural habitats and captivity conditions occupied by any given host species has not been captured in these comparisons. Moreover, intraspecific variation in gut microbiota, generally attributed to diet, may also stem from differential acquisition of environmental microbes—an understudied mechanism by which host microbiomes are directly shaped by environmental microbes. To more comprehensively characterize gut microbiota in an ecologically flexible host, the ring-tailed lemur (Lemur catta; n = 209), while also investigating the role of environmental acquisition, we used 16S rRNA sequencing of lemur gut and soil microbiota sampled from up to 13 settings, eight in the wilderness of Madagascar and five in captivity in Madagascar or the U.S. Based on matched fecal and soil samples, we used microbial source tracking to examine covariation between the two types of consortia.ResultsThe diversity of lemur gut microbes varied markedly within and between settings. Microbial diversity was not consistently greater in wild than in captive lemurs, indicating that this metric is not necessarily an indicator of host habitat or environmental condition. Variation in microbial composition was inconsistent both with a single, representative gut community for wild conspecifics and with a universal ‘signal of captivity’ that homogenizes the gut consortia of captive animals. Despite the similar, commercial diets of captive lemurs on both continents, lemur gut microbiomes within Madagascar were compositionally most similar, suggesting that non-dietary factors govern some of the variability. In particular, soil microbial communities varied across geographic locations, with the few samples from different continents being the most distinct, and there was significant and context-specific covariation between gut and soil microbiota.ConclusionsAs one of the broadest, single-species investigations of primate microbiota, our study highlights that gut consortia are sensitive to multiple scales of environmental differences. This finding begs a reevaluation of the simple ‘captive vs. wild’ dichotomy. Beyond the important implications for animal care, health, and conservation, our finding that environmental acquisition may mediate aspects of host-associated consortia further expands the framework for how host-associated and environmental microbes interact across different microbial landscapes.

Effects of Maternal Factors and Postpartum Environment on Early Colonization of Intestinal Microbiota in Piglets.

Intestinal microbiota significantly influences the intake, storage, and utilization of body nutrients, as well as animal growth and development. The establishment of microbiota is affected by many factors, such as delivery and feeding modes, antibiotics, disease, and the surrounding environment. In this study, we selected Chinese indigenous Mashen and Jinfen White pigs as the study subjects. To explore the source and factors affecting the piglet intestinal microbiota, 16S rRNA gene sequencing was performed to analyze the microbial composition of the feces, saliva, vaginal secretions, and colostrum of parturient sows, feces and saliva of newborn piglets, and surrounding environment samples. The results showed that the microbiota of the saliva of sows and piglets is structurally similar to that of the environment and is dominated by the phylum Proteobacteria, including Acinetobacter, Actinomyces, and Pseudomonas. The core genus in the vaginal secretions and colostrum of sows was Pseudomonas. Among the fecal samples, the core bacterial genera in sows before and after delivery were Clostridium sensu_stricto_1 and Christensenellaceae_R-7_group, while in piglets at 1 d of age, Pseudomonas and Escherichia-Shigella were most abundant. These results indicate that microbiota in feces, colostrum, and vaginal secretions of sows more easily colonized piglet intestines through a symbiotic effect. The environmental and salivary microbiota could also affect the early colonization and succession of the intestinal microbiota of piglets to some extent. This study provides a theoretical basis for sow delivery protection and early nursing of piglets and background for the research and development of microbial agents to improve piglet intestinal health.

A practical guide for restoration ecologists to manage microbial contamination risks before laboratory processes during microbiota restoration studies

Environmental microbiota are becoming more conventional components of restoration ecology studies due to their functional importance in ecosystems. Studying these microbiota offers insight into how they respond to, and potentially drive, ecosystem restoration. However, microbes are everywhere and therefore they pose a risk to sample integrity via uncontrolled contamination, and many of these risks are introduced before entering a molecular facility. Field ecologists who have limited experience in microbial and/or molecular studies may lack the knowledge on how to mitigate microbial contamination risks and, accordingly, may find rigorous collection of microbial samples a daunting task. Here, we present a practical guide that builds on our previous paper to help manage the risks of microbial contamination when undertaking a microbiota restoration study prior to entering a molecular facility. We cover study design and planning, undertaking field sampling, and sample transport and storage. We hope to provide a useful and practical guide to restoration ecologists who wish to include a microbiota component in their studies. If done well, this inclusion offers improved research quality and ultimately enhanced restoration outcomes.

Spatiotemporal distribution of environmental microbiota in spontaneous fermentation workshop: The case of Chinese Baijiu

The strong-flavor Baijiu (SFB) brewing workshop is a complex ecosystem with diverse microbiomes. As a potential source of microbiomes in fermentation, microbiota in the environmental microecology may affect the quality and flavor of SFB. Here, we report the collection of environmental microecological samples from three SFB workshops with different usage times (named 70a, 30a, and new, respectively). We used 16S rRNA and internal transcribed spacer (ITS) gene amplicon full-length sequencing to explore the microbial community structure in SFB. The SourceTracker tool was used to investigate links among fermentation samples, raw materials, and the environment and decipher the construction process in the workshop indoor environment. Lactobacillus acetotolerans was the most important bacterial genus in Zaopei after fermentation, whereas other types of samples exhibited different prokaryotic community structures. The composition of the fungal community was similar, with Saccharomycopsis fibuligera, Debaryomyces hansenii, Lichtheimia ramosa, Lichtheimia corymbifera, and Pichia kudriavzevii being the most abundant, and were detected in most samples. Further comparison of the microbiota in the workshop environment showed that the diversity of the microbiota in the indoor environment decreased, showing different clustering patterns under the influence of location. With increasing usage time, the contribution of deterministic processes to the assembly of the prokaryotic community increases, and the community structure tends to stabilize, exhibiting its own characteristics. SFB-fermenting resident functional fungi were the major components of the fungal community, and SourceTracker analysis also highlighted the contributions of Zaopei, Daqu, and tool surfaces as fungal sources. This study is the first to comprehensively monitor the microbial profile of the SFB production environment. This research can be extended to involve more complex spontaneous fermentation environment microbiota and has important implications for the control of spontaneous fermentation.

Comparative analysis of surface sanitization protocols on the bacterial community structures in the hospital environment

ObjectivesIn hospital hygiene, it remains unclear to what extent surface contamination might represent a potential reservoir for nosocomial pathogens. This study investigates the effects of different sanitization strategies on the microbial structures and the ecological balance of the environmental microbiome in the clinical setting. MethodsThree cleaning regimes (disinfectants, detergents, and probiotics) were applied subsequently in nine independent patient rooms at a neurological ward (Charité, Berlin). Weekly sampling procedures included three different environmental sites: floor, door handle, and sink. Characterization of the environmental microbiota and detection of antibiotic resistance genes (ARGs) were performed by 16S rRNA sequencing and multiplex Taq-Man qPCR assays, respectively. ResultsOur results showed a displacement of the intrinsic environmental microbiota after probiotic sanitization, which reached statistical significance in the sink samples (median 16S-rRNA copies = 138.3; IQR: 24.38–379.5) when compared to traditional disinfection measures (median 16S rRNA copies = 1343; IQR: 330.9–9479; p < 0.05). This effect was concomitant with a significant increase in the alpha-diversity metrics in both the floor (p < 0.001) and the sink samples (p < 0.01) during the probiotic strategy. We did not observe a sanitization-dependent change in relative pathogen abundance at any tested site, but there was a significant reduction in the total ARG counts in the sink samples during probiotic cleaning (mean ARGs/sample: 0.095 ± 0.067) when compared to the disinfection strategy (mean ARGs/sample: 0.386 ± 0.116; p < 0.01). DiscussionThe data presented in this study suggest that probiotic sanitization is an interesting strategy in hospital hygiene management to be further analyzed and validated in randomized clinical studies.

New Insights and Advances in Pathogenesis and Treatment of Very Early Onset Inflammatory Bowel Disease.

Very early onset inflammatory bowel disease (VEO-IBD) is characterized by multifactorial chronic recurrent intestinal inflammation. Compared with elderly patients, those with VEO-IBD have a more serious condition, not responsive to conventional treatments, with a poor prognosis. Recent studies found that genetic and immunologic abnormalities are closely related to VEO-IBD. Intestinal immune homeostasis monogenic defects (IIHMDs) are changed through various mechanisms. Recent studies have also revealed that abnormalities in genes and immune molecular mechanisms are closely related to VEO-IBD. IIHMDs change through various mechanisms. Epigenetic factors can mediate the interaction between the environment and genome, and genetic factors and immune molecules may be involved in the pathogenesis of the environment and gut microbiota. These discoveries will provide new directions and ideas for the treatment of VEO-IBD.