High-throughput 16S rRNA Gene Research Articles

Impact of earthworms on antibiotic resistance genes removal in ampicillin-contaminated soil through bacterial community alteration.

The emergence of antibiotic resistance genes (ARGs) as contaminants in soil poses a significant threat to public health. Earthworms (Eisenia foetida), which are common inhabitants of soil, have been extensively studied for their influence on ARGs. However, the specific impact of earthworms on penicillin-related ARGs remains unclear. In this study, we investigate the role of earthworms in mitigating ARGs, specifically penicillin-related ARGs, in ampicillin-contaminated soil. Utilizing high-throughput quantitative PCR (HT-qPCR), we quantified a significant reduction in the relative abundance of penicillin-related ARGs in soil treated with earthworms, showing a decrease with a p-value of <0.01. Furthermore, high-throughput 16S rRNA gene sequencing revealed that earthworm intervention markedly alters the microbial community structure, notably enhancing the prevalence of specific bacterial phyla such as Proteobacteria, Firmicutes, Chloroflexi, and Tenericutes. Our findings not only demonstrate the effectiveness of earthworms in reducing the environmental load of penicillin-related ARGs but also provide insight into the alteration of microbial communities as a potential mechanism. This research contributes to our understanding of the role of earthworms in mitigating the spread of antibiotic resistance and provides valuable insights for the development of strategies to combat this global health issue.

Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA.

Lehman Caves is an extensively decorated high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with δ34SV-CDT between +9.7‰ and +26.1‰, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later-stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of desert hypogene cave systems.

Expanding oxygen minimum zones in the northern Indian Ocean predicted by hypoxia-related bacteria

Oxygen minimum zones (OMZs) in the ocean are areas with dissolved oxygen (DO) concentrations below critical thresholds that impact marine ecosystems and biogeochemical cycling. In the northern Indian Ocean (NIO), OMZs exhibit a tendency to expand in mesopelagic waters and contribute significantly to global nitrogen loss and climate change. However, the microbial drivers of OMZ expansion in the NIO remain understudied. Here, we characterized bacterial communities across DO gradients in the NIO using high-throughput 16S rRNA gene sequencing. We found that Marinimicrobia, Chloroflexi, and the SAR324 clade were enriched in both oxygen-deficient and low oxygen mesopelagic waters. Furthermore, Marinimicrobia, Chloroflexi, and the SAR324 clade exhibited a significant negative correlation with DO (P &amp;lt; 0.01), suggesting that they were well-adapted to the oxygen-deficient OMZ habitat. Functional predictions revealed heightened nitrogen metabolism in OMZs, particularly nitrate reduction, suggesting its pivotal role in nitrogen loss. These findings underscore the importance of microbial communities in driving OMZ expansion in the NIO and highlight their implications in global biogeochemical cycles and climate change.

Is redox zonation an appropriate method for determining the stage of natural remediation in deep contaminated groundwater?

Groundwater contamination resulting from petroleum development poses a significant threat to drinking water sources, especially in developing countries. In situ natural remediation methods, including microbiological processes, have gained popularity for the reduction of groundwater contaminants. However, assessing the stage of remediation in deep contaminated groundwater is challenging and costly due to the complexity of diverse geological conditions and unknown initial concentrations of contaminants. This research proposes that redox zonation may be a more convenient and comprehensive indicator than the concentration of contaminants for determining the stage of natural remediation in deep groundwater. The combination of sequencing microbial composition using the high-throughput 16S rRNA gene and function predicted by FAPROTAX is a useful approach to determining the redox conditions of different contaminated groundwater. The sulfate-reducing environment, represented by Desulfobacteraceae, Peptococcaceae, Desulfovibrionaceae, and Desulfohalobiaceae could be used as characteristic early stages of remediation for produced water contamination in wells with high concentrations of SO42−, benzene, and salinity. The nitrate-reducing environment, enriched with microorganisms related to denitrification, sulfur-oxidizing, and methanophilic microorganisms could be indicative of the mid stages of in situ bioremediation. The oxygen reduction environment, enriched with oligotrophic and pathogenic Sphingomonadaceae, Caulobacteraceae, Syntrophaceae, Legionellales, Moraxellaceae, and Coxiellaceae, could be indicative of the late stages of remediation. This comprehensive approach could provide valuable insights into the process of natural remediation and facilitate improved environmental management in areas of deep contaminated groundwater.

Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands.

Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.

Multiple approaches in the study of ancient human microbiome

Abstract Research related to the analysis of microbial communities in ancient human samples began two decades ago. Since then, new technologies as well as new bioinformatic tools have been developed for the manipulation of massive data. All this together, with the theoretical knowledge generated from microbial ecology has expanded our understanding of the human microbiome. Despite the challenge of studying ancient samples and their microbiome, some approaches applied to the contemporary human microbiome have been successfully applied to ancient samples. Most studies in ancient samples have focused on taxonomic profiling at the community level with metagenomic or high-throughput 16S rRNA gene amplicon sequencing data. However, other approaches have emerged in order to get deeper understanding of the ancient human microbiome. Therefore, the aim of this review is to discuss all the approaches and methodologies successfully applied to ancient samples and ancient microbiome as well as the information that can be generated using them, in order to understand the evolution of human microbiome interactions throughout history.

Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes.

Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils.

Dietary Galacto-oligosaccharides Ameliorate Atopic Dermatitis-like Skin Inflammation and Behavioral Deficits by Modulating Gut Microbiota-Brain-Skin Axis.

Atopic dermatitis (AD), a chronic, highly pruritic, and inflammatory skin disorder, often coexists with psychiatric comorbidities including anxiety and depression, posing considerable challenges for treatment. The current research aims at evaluating the efficacy and potential therapeutic mechanism of galacto-oligosaccharides (GOS) on AD-like skin lesions and comorbid anxiety/depressive disorders. Macroscopical and histopathological examination showed that GOS could markedly relieve skin inflammation by decreasing the production of IgE, IL-4, IL-13, IFN-γ, and TNF-α and regulating the PPAR-γ/NF-κB signaling in DNFB-induced AD mice. Moreover, GOS significantly improved the anxiety- and depressive-like symptoms as mirrored by the behavior tests including FST, TST, OFT, and EZM through normalizing the neurotransmitter levels of 5-HT, DA, NE, and CORT in the brain. Mechanistically, by virtue of the high-throughput 16S rRNA gene sequencing and GC-MS techniques, GOS restructured the gut microbiota and specifically induced the proliferation of Lactobacillus and Alloprevotella, leading to an increase in the total content of fecal SCFAs, in particular acetate and butyrate. Pearson correlation analysis found a marked correlation among the altered gut microbiota/SCFAs, AD-associated skin manifestations, and comorbid behavioral phenotypes. Collectively, this work highlights that GOS is a promising strategy against both AD and associated depressive symptoms by modulating the gut microbiota-brain-skin axis.

Effects of Bacillus coagulans TBC169 on gut microbiota and metabolites in gynecological laparoscopy patients.

The primary objective of this study is to investigate the mechanism by which Bacillus coagulans TBC169 accelerates intestinal function recovery in patients who have undergone gynecological laparoscopic surgery, using metabolomics and gut microbiota analysis. A total of 20 subjects were selected and randomly divided into two groups: the intervention group (n = 10) receiving Bacillus coagulans TBC169 Tablets (6 pills, 1.05 × 108 CFU), and the control group (n = 10) receiving placebos (6 pills). After the initial postoperative defecation, fecal samples were collected from each subject to analyze their gut microbiota and metabolic profiles by high-throughput 16S rRNA gene sequencing analysis and untargeted metabonomic. There were no statistically significant differences observed in the α-diversity and β-diversity between the two groups; however, in the intervention group, there was a significant reduction in the relative abundance of unclassified_Enterobacteriaceae at the genus level. Furthermore, the control group showed increased levels of Holdemanella and Enterobacter, whereas the intervention group exhibited elevated levels of Intestinimonas. And administration of Bacillus coagulans TBC169 led to variations in 2 metabolic pathways: D-glutamine and D-glutamate metabolism, and arginine biosynthesis. This study demonstrated that consuming Bacillus coagulans TBC169 after gynecological laparoscopic surgery might inhibit the proliferation of harmful Enterobacteriaceae; mainly influence 2 pathways including D-glutamine and D-glutamate metabolism, and arginine biosynthesis; and regulate metabolites related to immunity and intestinal motility; which can help regulate immune function, maintain intestinal balance, promote intestinal peristalsis, and thus accelerate the recovery of intestinal function.

487 - Adult atopic dermatitis is associated with impaired oral health and oral dysbiosis - a case-control study

Abstract Background Previous studies linked chronic oral diseases to skin disorders such as psoriasis. However, data about oral health and oral microbiota in atopic dermatitis (AD) is sparse. Objectives To compare the oral health status and oral microbiota of AD patients and healthy controls. Methods This was a prospective sex and age- matched case-control study comparing adult participants with and without dermatologist-verified AD. Exclusion criteria included recent use of oral, topical, or systemic medication that could affect oral health or microbiome assessment. Oral health indices including Gingival Index, Plaque Index, Oral Hygiene Index, Caries Severity Index and prosthodontics status, were assessed by a dentist. Samples of oral flora were collected and subjected to high-throughput 16S rRNA gene sequencing analysis for microbiome analysis. Results Forty-five AD participants and 41 non-AD controls were recruited. The two groups had no significant differences in terms of their demographic and clinical characteristics, except for the higher rate of atopic co-morbidities in the AD group (p&amp;lt;.001). Compared to the control group, participants with AD had significantly poorer plaque (p=0.04) and oral hygiene indices (p=0.04) and a trend towards higher gingival index (p=0.05). The results of the Faith phylogenetic diversity (FDR) test indicated that the oral microbial diversity in the AD group was significantly higher (α-diversity, FDR-adjusted p=0.0007) when compared with the control group. Characterization of the similarities and differences in the composition of the microbial communities between the samples (β-diversity) from the AD patients and controls indicated that they clustered separately. The groups showed significant dissimilarity and distinct clustering of microbial abundance (FDR-adjusted p=0.001). Importantly, higher community diversity was previously linked to periodontitis and gingival disease. Furthermore, AD patients had a significantly increased abundance of taxa correlated with oral diseases and decreased abundance of oral health-associated bacteria. Conclusion AD appears to be associated with poorer oral health and oral dysbiosis, and thus, there is a need to increase the awareness of both patients and physicians about oral health.

Rutaecarpine ameliorates imiquimod-induced psoriasis-like dermatitis in mice associated with alterations in the gut microbiota.

Psoriasis is accepted as a chronic, inflammatory, immune-mediated skin disease triggered by complex environmental and genetic factors. For a long time, disease recurrence, drug rejection, and high treatment costs have remained enormous challenges and burdens to patients and clinicians. Natural products with effective immunomodulatory and anti-inflammatory activities from medicinal plants have the potential to combat psoriasis and complications. Herein, an imiquimod (IMQ)-induced psoriasis-like dermatitis model is established in mice. The model mice are treated with 1% rutaecarpine (RUT) (external use) or the oral administration of RUT at different concentrations. Furthermore, high-throughput 16S rRNA gene sequencing is applied to analyze the changes in the diversity and composition of the gut microbiota. Based on the observation of mouse dorsal skin changes, RUT can protect against inflammation to improve psoriasis-like skin damage in mice. Additionally, RUT could suppress the expression levels of proinflammatory cytokines (IL-23, IL-17A, IL-22, IL-6, and IFN-α) within skin tissue samples. Concerning gut microbiota, we find obvious variations within the composition of gut microflora between IMQ-induced psoriasis mice and RUT-treated psoriasis mice. RUT effectively mediates the recovery of gut microbiota in mice induced by IMQ application. Psoriasis is linked to the production of several inflammatory cytokines and gut microbiome alterations. This research shows that RUT might restore gut microbiota homeostasis, reduce inflammatory cytokine production, and ameliorate psoriasis symptoms. In conclusion, the gut microbiota might be a therapeutic target or biomarker for psoriasis that aids in clinical diagnosis and therapy.

Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India.

The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 103CFU/mL) and ampicillin (≥ 8.128 × 103CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.

Fecal Microbiota and Feeding Habitats of Nomadic Indigenous Animals (Deer, Yak, Sheep and Camel) in Baikal Siberia (Russia)

In the vast expanse of Baikal Siberia, indigenous nomadic animal groups have been conserved, grazing on pastures throughout the year. It is believed that the fecal microbiota of these diverse nomadic animal species is unique to each species and closely tied to their feeding environments. We conducted a pioneering comparative analysis of the taxonomic structure and the diversity of fecal microbiota in indigenous nomadic animals inhabiting Baikal Siberia. Our study encompassed 20 deer, 23 yaks, 24 camels, and 29 sheep, using high-throughput 16S rRNA gene profiling. In the fecal microbiota of these animals, we observed a predominant presence of the phyla Bacillota, Bacteroidota, and Verrucomicrobiota, collectively comprising over 88% of the microbial communities. Moreover, these proportions exhibited variations according to the host species. The unculturable Bacillota UCG-005 and UCG-010 are the key groups for all animals. However, at the genus level, distinctive compositions of fecal microbiota were discernible within each animal group. We identified a total of 37 dominant genera across the fecal samples from these four animal species. Principal component analysis (PCA) and cluster analysis demonstrated that the fecal microbiota composition clustered among individuals of the same animal species. Linear discriminant analysis effect size (LEfSe) indicated that camels exhibited higher abundances of the family Akkermansiaceae and the uncultured clostridial lineage UCG-010, while deer featured Lachnospiraceae; sheep had Ruminococcaceae; and yaks displayed Monoglobaceae, Bacteroidaceae, and methanogenic archaea from the family Methanobacteriaceae as distinctive marker taxa. Our studies showed that the studied nomadic animals feed mainly on plants belonging to the families Poaceae, Cyperaceae, Asteraceae, and Rosaceae. Our research indicated that the identity of the host species and, to a lesser degree, their diets and habitats, significantly shape the composition of fecal microbiota in these studied nomadic ruminant animals.

The microbial and metabolite composition of Gouda cheese made from pasteurized milk is determined by the processing chain

Gouda cheeses of different production batches and ripening times often differ in metabolite composition, which may be due to the starter culture mixture applied or the growth of non-starter lactic acid bacteria (NSLAB) upon maturation. Therefore, a single Gouda cheese production batch was systematically investigated from the thermized milk to the mature cheeses, ripened for up to 100 weeks, to identify the main bacterial species and metabolites and their dynamics during the whole production and ripening. As this seemed to be starter culture strain- and NSLAB-dependent, it requested a detailed, longitudinal, and quantitative investigation. Hereto, microbial colony enumeration, high-throughput full-length 16S rRNA gene sequencing, and a metabolomic approach were combined. Culture-dependently, Lactococcus lactis was the most abundant species from its addition as part of the starter culture up to the first two months of cheese ripening. Afterward, the NSLAB Lacticaseibacillus paracasei became the main species during ripening. The milk was a possible inoculation source for the latter species, despite pasteurization. Culture-independently, the starter LAB Lactococcus cremoris and Lc. lactis were the most abundant species in the cheese core throughout the whole fermentation and ripening phases up to 100 weeks. The cheese rind from 40 until 100 weeks of ripening was characterized by a high relative abundance of the NSLAB Tetragenococcus halophilus and Loigolactobacillus rennini, which both came from the brine. These species were linked with the production of the biogenic amines cadaverine and putrescine. The most abundant volatile organic compound was acetoin, an indicator of citrate and lactose fermentation during the production day, whereas the concentrations of free amino acids were an indicator of the ripening time.

Evaluation of the antibacterial effect of Epigallocatechin gallate on the major pathogens of canine periodontal disease and therapeutic effects on periodontal disease mice.

Periodontal disease (PD) is a prevalent oral affliction in canines, with limited therapeutic options available. The potential transmission of oral bacteria from canines to humans through inter-species contact poses a risk of zoonotic infection. Epigallocatechin gallate (EGCG), the principal catechin in green tea polyphenols, exhibits antibacterial properties effective against human PD. Given the clinical parallels between canine and human PD, this study explores the feasibility of employing EGCG as a therapeutic agent for canine PD. Initially, a survey and statistical analysis of bacterial infection data related to canine PD in China were conducted. Subsequently, the primary pathogenic bacteria of canine PD were isolated and cultivated, and the in vitro antibacterial efficacy of EGCG was assessed. Furthermore, verify the therapeutic effect of EGCG on a mouse PD model in vivo. The high-throughput 16S rRNA gene sequencing identified Porphyromonas, Fusobacterium, Treponema, Moraxella, and Capnocytophaga as the genera that distinguishing PD from healthy canines' gingival crevicular fluid (GCF) samples in China. The anaerobic culture and drug susceptibility testing isolated a total of 92 clinical strains, representing 22 species, from 72 canine GCF samples, including Porphyromonas gulae, Prevotella intermedia, Porphyromonas macacae, etc. The minimum inhibitory concentration (MIC) ranging of EGCG was from 0.019 to 1.25 mg/mL. Following a 7 days oral mucosal administration of medium-dose EGCG (0.625 mg/mL), the abundance of periodontal microorganisms in PD mice significantly decreased. This intervention ameliorated alveolar bone loss, reducing the average cementoenamel junction to the alveolar bone crest (CEJ-ABC) distance from 0.306 mm ± 0.050 mm to 0.161 mm ± 0.026 mm. Additionally, EGCG (0.3125 mg/mL) markedly down-regulated the expression of inflammatory factor IL-6 in the serum of PD mice. Our research demonstrates the significant antibacterial effects of EGCG against the prevalent bacterium P. gulae in canine PD. Moreover, EGCG exhibits anti-inflammatory properties and proves effective in addressing bone loss in a PD mouse model. These findings collectively suggest the therapeutic potential of EGCG in the treatment of canine PD. The outcomes of this study contribute valuable data, laying the foundation for further exploration and screening of alternative antibiotic drugs to advance the management of canine PD.

Human gut microbiota fermentation of cooked eggplant, garlic, and onion supports distinct microbial communities.

Heating and cooking vegetables not only enhances their palatability but also modifies their chemical structure, which in turn might affect their fermentation by resident gut microbes. Three commonly consumed vegetables that are known to undergo chemical browning, also known as Maillard reaction, during cooking - eggplant, garlic, and onion - were each fried, grilled, or roasted. The cooked vegetables were then subjected to an in vitro digestion-fermentation process aimed to simulate the passage of food through the human oro-gastro-intestinal tract. In the last step, the undigested fractions of these foods were anaerobically fermented by the complex human gut microbiota. We assessed the structure of microbial communities maintained on each cooked vegetable by high-throughput 16S rRNA gene amplicon sequencing, measured the levels of furosine, a chemical marker of the Maillard browning reaction, by HPLC, and determined the antioxidant capacities in all samples with ABTS and FRAP methods. Overall, vegetable type had the largest, statistically significant, effect on the microbiota structure followed by the cooking method. Onion fermentation supported a more beneficial community including an expansion of Bifidobacterium members and inhibition of Enterobacteriaceae. Fermentation of cooked garlic promoted Faecalibacterium growth. Among cooking methods, roasting led to a much higher ratio of beneficial-to-detrimental microbes in comparison with grilling and frying, possibly due to the exclusion of any cooking oil in the cooking process.

Mulberry (Morus alba L.) leaf water extract attenuates type 2 diabetes mellitus by regulating gut microbiota dysbiosis, lipopolysaccharide elevation and endocannabinoid system disorder

Ethnopharmacological relevanceMulberry (Morus alba L.) leaf is a well-known herbal medicine and has been used to treat diabetes in China for thousands of years. Our previous studies have proven mulberry leaf water extract (MLWE) could improve type 2 diabetes mellitus (T2D). However, it is still unclear whether MLWE could mitigate T2D by regulating gut microbiota dysbiosis and thereof improve intestinal permeability and metabolic dysfunction through modulation of lipopolysaccharide (LPS) and endocannabinoid system (eCBs). Aim of studyThis study aims to explore the potential mechanism of MLWE on the regulation of metabolic function disorder of T2D mice from the aspects of gut microbiota, LPS and eCBs. Materials and methodsGut microbiota was analyzed by high-throughput 16S rRNA gene sequencing. LPS, N-arachidonoylethanolamine (AEA) and 2-ararchidonylglycerol (2-AG) contents in blood were determined by kits or liquid phase chromatography coupled with triple quadrupole tandem mass spectrometry, respectively. The receptors, enzymes or tight junction protein related to eCBs or gut barrier were detected by RT-PCR or Western blot, respectively. ResultsMLWE reduced the serum levels of AEA, 2-AG and LPS, decreased the expressions of N-acylphophatidylethanolamine phospholipase D, diacylglycerol lipase-α and cyclooxygenase 2, and increased the expressions of fatty acid amide hydrolase (FAAH), N-acylethanolamine-hydrolyzing acid amidase (NAAA), alpha/beta hydrolases domain 6/12 in the liver and ileum and occludin, monoacylglycerol lipase and cannabinoid receptor 1 in the ileum of T2D mice. Furthermore, MLWE could change the abundances of the genera including Acetatifactor, Anaerovorax, Bilophila, Colidextribacter, Dubosiella, Gastranaerophilales, Lachnospiraceae_NK4A136_group, Oscillibacter and Rikenella related to LPS, AEA and/or 2-AG. Moreover, obvious improvement of MLWE treatment on serum AEA level, ileum occludin expression, and liver FAAH and NAAA expression could be observed in germ-free-mimic T2D mice. ConclusionMLWE could ameliorate intestinal permeability, inflammation, and glucose and lipid metabolism imbalance of T2D by regulating gut microbiota, LPS and eCBs.

Microbiome profile of the Antarctic clam Laternula elliptica.

The filter feeder clam Laternula elliptica is a key species in the Antarctic ecosystem. As a stenothermal benthic species, it has a poor capacity for adaptation to small temperature variations. Despite their ecological importance and sensitivity to climate change, studies on their microbiomes are lacking. The goal of this study was to characterize the bacterial communities of L. elliptica and the tissues variability of this microbiome to provide an initial insight of host-microbiota interactions. We investigated the diversity and taxonomic composition of bacterial communities of L. elliptica from five regions of the body using high-throughput 16S rRNA gene sequencing. The results showed that the microbiome of L. elliptica tended to differ from that of the surrounding seawater samples. However, there were no significant differences in the microbial composition between the body sites, and only two OTUs were present in all samples, being considered core microbiome (genus Moritella and Polaribacter). No significant differences were detected in diversity indexes among tissues (mean 626.85 for observed OTUs, 628.89 Chao1, 5.42 Shannon, and 0.87 Simpson). Rarefaction analysis revealed that most tissues reached a plateau of OTU number according to sample increase, with the exception of Siphon samples. Psychromonas and Psychrilyobacter were particularly abundant in L. elliptica whereas Fluviicola dominated seawater and siphons. Typical polar bacteria were Polaribacter, Shewanella, Colwellia, and Moritella. We detected the prevalence of pathogenic bacterial sequences, particularly in the family Arcobacteraceae, Pseudomonadaceae, and Mycoplasmataceae. The prokaryotic diversity was similar among tissues, as well as their taxonomic composition, suggesting a homogeneity of the microbiome along L. elliptica body.The Antarctic clam population can be used to monitor the impact of human activity in areas near Antarctic stations that discharge wastewater.

Compositional shifts in rhizobacterial communities of Brassica napus under salinity stress

Salinity stress severely limits crop production globally. The plant rhizosphere harbors diverse microbial communities that can positively influence plant growth and stress tolerance. Therefore, we examined the rhizosphere bacterial populations of Brassica napus under normal and saline conditions using high-throughput 16S rRNA gene sequencing. The objectives were set to identify key taxa enriched in the rhizosphere and evaluate variations in community structure between control and salt-stressed Brassica napus plants. Proteobacteria, Actinobacteria, Chloroflexi, and Bacteroidetes were the predominant phyla. Key genera enriched in the rhizosphere included Sphingomonas, Streptomyces, Bacillus, and Pseudomonas. Salinity stress increased the abundances of Chloroflexi and Acidobacteria while decreased Actinobacteria. Rhizosphere communities of salt-treated plants showed lower diversity but separate clusters from controls, indicating salinity-induced shifts. Predictive functional analysis revealed that amino acid/carbohydrate metabolism and membrane transport pathways in salt-stressed rhizospheres were elevated. This study provides novel insights into the rhizosphere bacteriome of Brassica napus under salinity, highlighting potential plant-growth-promoting taxa for stress amelioration.

Disentangling microbial coupled fillers mechanisms for the permeable layer optimization process in multi-soil-layering systems

The multi-soil-layering (MSL) systems is an emerging solution for environmentally-friendly and cost-effective treatment of decentralized rural domestic wastewater. However, the role of the seemingly simple permeable layer has been overlooked, potentially holding the breakthroughs or directions to addressing suboptimal nitrogen removal performance in MSL systems. In this paper, the mechanism among diverse substrates (zeolite, green zeolite and biological ceramsite) coupled microorganisms in different systems (activated bacterial powder and activated sludge) for rural domestic wastewater purification was investigated. The removal efficiencies performed by zeolite coupled with microorganisms within 3 days were 93.8% for COD, 97.1% for TP, and 98.8% for NH4+-N. Notably, activated sludge showed better nitrification and comprehensive performance than specialized nitrifying bacteria powder. Zeolite attained an impressive 89.4% NH4+-N desorption efficiency, with a substantive fraction of NH4+-N manifesting as exchanged ammonium. High-throughput 16S rRNA gene sequencing revealed that aerobic and parthenogenetic anaerobic bacteria dominated the reactor, with anaerobic bacteria conspicuously absent. And the heterotrophic nitrification-aerobic denitrification (HN-AD) process was significant, with the presence of denitrifying phosphorus-accumulating organisms (DPAOs) for simultaneous nitrogen and phosphorus removal. This study not only raises awareness about the importance of the permeable layer and enhances comprehension of the HN-AD mechanism in MSL systems, but also provides valuable insights for optimizing MSL system construction, operation, and rural domestic wastewater treatment.