The Mechanism of Arsenic Release in Contaminated Paddy Soil with Added Biochar: The Role of Dissolved Organic Matter, Fe, and Bacteria.

The addition of biochar inevitably modifies the acidity (pH), redox potential (Eh), and dissolved organic matter (DOM) level in the soil. These alterations also have coupled effects on the cycling of iron (Fe) and the composition of bacterial communities, thereby impacting the speciation and availability of arsenic (As) in the soil. This study explored the potential mechanisms through which biochar affects As in paddy soil during flooded cultivation with different pyrolysis temperature biochars (300 °C, 400 °C, and 500 °C) added. The results revealed that the TAs concentration increased in the initial 15 days of soil cultivation with SBC300 or SBC400 addition because increasing the concentration of DOM induced the mobility of As though the formation of As-DOM complexes. Meanwhile, biochar addition elevated the pH, decreased the Eh, and promoted the transformation of specific adsorbed As (A-As) and amorphous iron oxide-bound As (Amo-Fe-As) to supernatant As through enhancing the reductive dissolution of Fe(oxy)(hydr)oxides. Moreover, the biochar altered the relative abundance of As (V)-reducing bacteria (such as Firmicutes) and As (III)-oxidizing bacteria (such as Chloroflex), thereby affecting As speciation. However, these mechanistic effects varied depending on the pyrolysis temperature of the biochar. The microbial composition of SBC300 and SBC400 were similar, with both containing larger populations of Enterobacteriaceae (AsRB) and pseudomonas (FeRB) compared to CK and SBC500. It was proposed that lower pyrolysis temperatures (300 °C and 400 °C) are more favorable for the dissolution of Fe(oxy)(hydr)oxides and the reduction of As (V). However, the biochar from the higher pyrolysis temperature (500 °C) showed environmental impacts akin to the control group (CK). This study demonstrated potential mechanisms of biochar's effect on As and the role of pyrolysis temperature.

Impact of including two types of destoned olive cakes in pigs' diets on fecal bacterial composition and study of the relationship between fecal microbiota, feed efficiency, gut fermentation, and gaseous emissions.

The microbial population in the pig's gastrointestinal tract can be influenced by incorporating fibrous by-products into the diets. This study investigated the impact of including two types of dried olive cake (OC) in pigs' diets on fecal bacterial composition. The correlation between fecal microbiota and growth performance, nutrient digestibility, gut fermentation pattern and slurry gas emissions was also evaluated. Thirty male Pietrain x (Landrace x Large white) pigs (47.9 ± 4.21 kg) were assigned to three groups: a control group (C), a group fed a diet with 20% partially defatted OC (20PDOC), and a group fed a diet with 20% cyclone OC (20COC) for 21 days. Fecal samples collected before and after providing the experimental diets were analyzed for the V3-V4 region of the 16S rRNA gene. Pigs were weighed, and feed intake was recorded throughout the study. Potential ammonia and methane emissions from slurry were measured. No significant differences in alpha diversity indexes were found. The taxonomic analysis revealed that Firmicutes and Bacteroidota phyla were dominant at the phylum level across all groups. Differential abundance analysis using ALDEx showed significant differences among groups for various bacteria at the phylum, genus, and species levels at the end of the experiment. Pigs from 20PDOC and 20COC groups exhibited increased abundances of health-promoting bacteria, such as Plactomycetota at the phylum level and Allisonella and an unidentified genus from the Eggerthellaceae family at the genus level. These changes influenced short-chain fatty acids' (SCFA) concentration in slurries, leading to greater acetic, butyric, caproic and heptanoic acids in OC-fed groups, especially 20COC pigs. A volatility analysis revealed significant positive correlations (p < 0.05) between Uncultured_Bacteroidales and Unculured_Selenomonadaceae and energy digestibility. Monoglobus and Desulfovibrio showed a positive significant (p < 0.05) correlation with total SCFA, indicating a high impact on gut fermentation. However, growth performance parameters and potential gas emission displayed no significant correlations with a specific bacterial genus. In conclusion, our results suggest that OC inclusion into pig diets could positively modulate and contribute to the gut microbiota's favorable composition and functionality. Also, nutrient digestibility and gut fermentation patterns can be associated with specific microbial populations.

An updated study of the relationship between bacterial infections and women's immune system, focusing on bacterial compositions with successful pregnancy.

Genital tract infections can cause a variety of harmful health outcomes, including endometritis, bacterial vaginosis, and pelvic inflammatory disease, in addition to infertility. Anaerobic bacteria, such as Gardnerella vaginalis, Megasphaera spp., and Atopobium vaginae, are more commonly identified in cases of bacterial vaginosis than lactobacilli. It is unknown how the microorganisms that cause pelvic inflammatory diseases and endometritis enter the uterus. Both prospective and retrospective research have connected pelvic inflammatory disorders, chronic endometritis, and bacterial vaginosis to infertility. Similar to bacterial vaginosis, endometritis-related infertility is probably caused by a variety of factors, such as inflammation, immune system recognition of sperm antigens, bacterial toxins, and a higher risk of STDs. Preconception care for symptomatic women may include diagnosing and treating pelvic inflammatory disease, chronic endometritis, and bacterial vaginosis before conception to optimize the results of both natural and assisted reproduction.

Impact of cultivating different Ocimum species on bioaerosol bacterial communities and functional genome at an agricultural site.

The effects of the surrounding environment on the bacterial composition of bioaerosol were well documented for polluted and contaminated sites. However, there is limited data on the impact of plant species, especially those that produce aromas, on bioaerosol composition at agricultural sites. Hence, the aim of this study is to evaluate the variability in bacterial communities present in bioaerosol samples collected from agricultural sites with aroma-producing crops. For this, PM2.5, PM10, and bioaerosol samples were collected from agricultural fields growing Ocimum [two varieties of O. sanctum (CIM-Aayu and CIM-Angana)] and O. kilimandscharicum (Kapoor), nearby traffic junctions and suburban areas. PM2.5 and PM10 concentrations at the agricultural site were in between the other two polluted sites. However, bioaerosol concentration was lower at agricultural sites than at other sites. The culturable bacteria Bacillus subtilis, Bacillus tequilensis, and Staphylococcus saprophyticus were more prevalent in agricultural sites than in other areas. However, the composition of non-culturable bacteria varied between sites and differed in three fields where Ocimum was cultivated. The CIM-Aayu cultivated area showed a high bacterial richness, lower Simpson and Shannon indices, and a distinctive metabolic profile. The sites CIM-Angana and CIM-Kapoor had a higher abundance of Aeromonas, while Pantoea and Pseudomonas were present at CIM-Aayu. Acinetobacter, Staphylococcus, and Bacillus were the dominant genera at the other two sites. Metabolic profiling showed that the CIM-Aayu site had a higher prevalence of pathways related to amino acid and carbohydrate metabolism and environmental information processing compared to other sites. The composition of bioaerosol among the three different Ocimum sites could be due to variations in the plant volatile and cross-feeding nature of bacterial isolates, which further needs to be explored.

Geographic Location Affects the Bacterial Community Composition and Diversity More than Species Identity for Tropical Tree Species.

Microorganisms associated with plants play a crucial role in their growth, development, and overall health. However, much remains unclear regarding the relative significance of tree species identity and spatial variation in shaping the distribution of plant bacterial communities across large tropical regions, as well as how these communities respond to environmental changes. In this study, we aimed to elucidate the characteristics of bacterial community composition in association with two rare and endangered tropical tree species, Dacrydium pectinatum and Vatica mangachapoi, across various geographical locations on Hainan Island. Our findings can be summarized as follows: (1) Significant differences existed in the bacterial composition between D. pectinatum and V. mangachapoi, as observed in the diversity of bacterial populations within the root endosphere. Plant host-related variables, such as nitrogen content, emerged as key drivers influencing leaf bacterial community compositions, underscoring the substantial impact of plant identity on bacterial composition. (2) Environmental factors associated with geographical locations, including temperature and soil pH, predominantly drove changes in both leaf and root-associated bacterial community compositions. These findings underscored the influence of geographical locations on shaping plant-associated bacterial communities. (3) Further analysis revealed that geographical locations exerted a greater influence than tree species identity on bacterial community compositions and diversity. Overall, our study underscores that environmental variables tied to geographical location primarily dictate changes in plant bacterial community composition. These insights contribute to our understanding of microbial biogeography in tropical regions and carry significant implications for the conservation of rare and endangered tropical trees.

Analysis of the Nasal Microbiota in Healthy and Diseased Pigs.

Massive sequencing of a fragment of 16S rRNA gene allows the characterization of bacterial communities in different body sites: the microbiota. Nasal microbiota can be analyzed by DNA extraction from nasal swabs, amplification of the specific fragment of interest, and posterior sequencing. The raw sequences obtained need to go through a computational process to check their quality and then assign the taxonomy. Here, we will describe the complete process from sampling to get the microbial diversity of nasal microbiota in health and disease.

Supplementation of Methionine Dipeptide Enhances the Milking Performance of Lactating Dairy Cows.

Methionine dipeptide (Met-Met) could improve milk protein synthesis in bovine epithelia mammary cells and lactating mice, while the effects of Met-Met on lactation performance, rumen fermentation and microbiota profile in lactating dairy cows have not been explored. For this reason, 60 Chinese lactating Holstein cows were allocated into three treatment groups: control group (CON), 6 g/d methionine dipeptide group (MM), and 6.12 g/d rumen-protected methionine dipeptide group (RPMM). The experiment lasted for 10 weeks to monitor lactation performance, plasma amino acid profile and rumen fermentation parameters and microbiota profile. Results showed that MM increased the energy-corrected milk (ECM), and RPMM increased both milk yield and ECM (p < 0.05). The milk protein concentration and yield were increased by MM and RPMM (p < 0.05). The rumen fermentation showed that RPMM increased total volatile fatty acids, acetate and valerate concentrations (p < 0.05). The relative abundance of Firmicutes, including Succiniclasticum, Selenomonas and Clostridium_XlVa, were enriched and the Prevotella was decreased by RPMM (p < 0.05). In summary, daily supplementing with 6 g of MM or RPMM in lactating dairy cows could improve milk yield and both percentage and yield of milk protein, and RPMM benefited the rumen fermentation and altered the bacterial composition. These results provided the first evidence that Met-Met supplementation can improve lactation performance of dairy cows.

Inhibitory effects of glutathione peroxidase on microbial spoilage of crayfish (Procambarus clarkii) during refrigerated storage.

The variety of enzyme-based biological preservatives is limited. This study evaluated the effects of glutathione peroxidase (GSH-Px) on the quality of crayfish during refrigerated storage by measuring the pH, total volatile basic nitrogen, trimethylamine, and microbial contamination in crayfish muscle simulation system. The results revealed that 0.3% GSH-Px (CK3) not only suppressed the degradation of nitrogenous substances but also decreased the contamination levels of total viable, Enterobacteriaceae, and Pseudomonas counts (P < 0.05). Furthermore, the populations of Lactococcus, Aeromonas, and Massilia differed in the CK3 group compared to the other groups (P < 0.05) at the end of the storage (day 15). Moreover, the principal coordinate analysis showed that the colony composition of CK3 stored for 15 days was similar to that of the control group stored for 10 days. Therefore, GSH-Px exhibits antibacterial activity against Gram-negative bacteria and has good application potential in freshwater aquatic product preservation.

The characteristics of the gut microbiota in patients with pulmonary tuberculosis: A systematic review.

Increasing evidence has indicated dysbiosis of the gut microbiota in patients with pulmonary tuberculosis (PTB). However, the change in the intestinal microbiota varies between different studies. This systematic review was conducted to investigate the characteristics of the gut microbiota in PTB patients. The MBASE, MEDLINE, Web of Science, and Cochrane Library electronic databases were systematically searched, and the quality of the retrieved studies was evaluated using the Newcastle-Ottawa scale. A total of 12 studies were finally included in the systematic review. Compared with healthy controls, the index reflecting α-diversity including the richness and/or diversity index decreased in 6 studies, while ß-diversity presented significant differences in PTB patients in 10 studies. Although the specific gut microbiota alterations were inconsistent, short-chain fatty acid-producing bacteria (including Lachnospiraceae, Ruminococcus, Blautia, Dorea, and Faecalibacterium), bacteria associated with an inflammatory state (e.g., Prevotellaceae and Prevotella), and beneficial bacteria (e.g., Bifidobacteriaceae and Bifidobacterium) were commonly noted. Our systematic review identifies key evidence for gut microbiota alterations in PTB patients, in comparison with healthy controls; however, no consistent conclusion could be drawn, due to the inconsistent results and heterogeneous methodologies of the enrolled studies. Therefore, more well-designed research with standard methodologies and large sample sizes is required.

Casein hydrolysate in naturally-fermented buckwheat sourdough: Effects on fermented and physicochemical characteristics, texture, and bacterial microbial composition.

The effect of a casein hydrolysate (CH) on the fermentation and quality of a naturally-fermented buckwheat sourdough (NFBS) were investigated, through assessing the fermentation characteristics, carbohydrate and protein degradation, texture, and bacterial composition of NFBS. According to the assaying data, CH might both increase the amount of lactic acid bacteria by 2.62 % and shorten the fermentation period by at least 3 h, subsequently leading to enhanced degradation of carbohydrate and protein, accompanied by a softer texture. More importantly, CH increased the relative abundance of lactobacillus in NFBS, making it the dominant bacterial genus and inhibited the growth of spoilage bacteria. In addition, Spearman correlation analysis indicated that the pH value, lactic and acetic acid contents, carbohydrates, protease activity, and these textural indices like hardness, elasticity, and adhesion had a positive/negative correlation with the bacterial composition of NFBS (Spearman correlation coefficient: -0.93-0.95). CH was thus regarded to be helpful to NFBS processing and production mainly by shortening its fermentation time, improving its fermentation performance, causing a finer texture and microstructure, and changing bacterial composition.

Liver cirrhosis and antibiotic therapy but not TIPS application leads to a shift of the intestinal bacterial communities: A controlled, prospective study.

OBJECTIVES: The gut-liver axis is discussed to play an important role in hepatic cirrhosis. Decompensated liver cirrhosis is associated with portal hypertension, which can lead to a variety of complications. Transjugular intrahepatic portosystemic shunt (TIPS) is an established treatment option for the complications of portal hypertension. In this study we focused on the effect of TIPS on intestinal microbial composition in cirrhotic patients. METHODS: Thirty patients with liver cirrhosis were compared to 18 healthy adults. Seventeen patients with cirrhosis and portal hypertension received a TIPS. Clinical characteristics, including age, sex, and liver function measured with a Child-Pugh score and model for end-stage liver disease score, were obtained. Intestinal microbial composition was assessed via 16S rRNA gene amplicon sequencing from stool probes before and after TIPS. RESULTS: TIPS led to a reduction of hepatic venous pressure gradient. However, TIPS did not cause a shift in the intestinal bacterial communities. Independent from the application of TIPS, antibiotic therapy was associated with a significant difference in the intestinal bacterial microbiota and also a reduced α-diversity. In addition, a significant difference was observed in the intestinal bacterial composition between patients with liver cirrhosis and healthy controls. CONCLUSION: The presence of liver cirrhosis and the use of antibiotic therapy, but not the application of TIPS, were associated with a significant shift of the intestinal bacterial communities, showing a high impact on the microbiota of patients with liver cirrhosis.

Microplastics inhibit the growth of endosymbiotic Symbiodinium tridacnidorum by altering photosynthesis and bacterial community.

Microplastics, ubiquitous anthropogenic marine pollutants, represent potential threats to coral-Symbiodiniaceae relationships in global reef ecosystems. However, the mechanism underlying the impacts of polystyrene microplastics (PS-MPs) on Symbiodiniaceae remains poorly understood. In this study, the cytological, physiological, and microbial responses of Symbiodinium tridacnidorum, a representative Symbiodiniaceae species, to varying concentrations of PS-MPs (0, 5, 50, 100, and 200 mg L-1) were investigated. The results revealed that microplastic exposure inhibited cell division, resulting in reduced cell density compared to control group. Furthermore, algal photosynthetic activity, as indicated by chlorophyll content, Fv/Fm, and net photosynthetic rate, declined with increasing microplastic concentration up to 50 mg L-1. Notably, elevated levels of microplastics (100 and 200 mg L-1) prompted a significant increase in cell size in S. tridacnidorum. Transmission electron microscopy and fluorescence microscopy indicated that hetero-aggregation was formed between high levels of PS-MPs and algal cells, ultimately causing damage to S. tridacnidorum. Moreover, the impact of PS-MPs exposure on the bacterial community associated with S. tridacnidorum was investigated. The results showed a reduction in alpha diversity of the bacterial community in groups exposed to 50, 100, and 200 mg L-1 of microplastics compared to those treated with 0 and 5 mg L-1. Additionally, the relative abundance of Marinobacter, Marivita, and Filomicrobium significantly increased, while Algiphilus and norank Nannocystaceae declined after microplastic exposure. These findings suggest that MPs can inhibit the growth of S. tridacnidorum and alter the associated bacterial community, posing a potential serious threat to coral symbiosis involving S. tridacnidorum.

Exploring the influence of garlic on microbial diversity and metabolite dynamics during kimchi fermentation.

Garlic (Allium sativum) is a key ingredient in Korean cuisine, particularly in the preparation of kimchi, contributing to its flavor and taste. Garlic has been a potential resource for lactic acid bacteria (LAB) in kimchi. However, the mechanism by which it influences microbial diversity and metabolite production is unclear. This study investigated the effect of garlic on the bacterial composition of and metabolite changes in kimchi. To achieve this, four separate batches of kimchi were prepared with varying garlic concentrations (w/w): 0 %, 1 %, 2 %, and 4 %, and the bacterial communities and metabolite production were monitored. In the early stages of fermentation, the count of LAB, operational taxonomic units (OTUs), and Shannon index increased linearly with the increase in garlic content. This indicated that garlic is a rich resource and contributes to the diversity of LAB during kimchi fermentation. Compared with the kimchi samples with a lower garlic content, those with a high garlic content (≥2 %) exhibited increased abundance of Lactobacillus and Leuconostoc as well as noticeable differences in functional diversity, including carbohydrate, amino acid, and energy metabolisms. Correlation analysis between sugars, organic acids, and predominant LAB in the garlic-containing kimchi samples suggested that in kimchi samples with high garlic content, LAB played a significant role in the fermentation process by metabolizing sugars and producing organic acids. Overall, this study demonstrated that the addition of garlic has a positive impact on the bacterial diversity and metabolite production during kimchi fermentation, potentially affecting the fermentation process and flavor profile of kimchi.

Effect of Yeast Inoculation on the Bacterial Community Structure in Reduced-Salt Harbin Dry Sausages: A Perspective of Fungi-Bacteria Interactions.

Yeast strains are promising starters to compensate for the flavor deficiencies of reduced-salt dry sausages, but their influence on the bacterial community's structure has not yet been clarified. In this study, the effect of separately inoculating Pichia kudriavzevii MDJ1 (Pk) and Debaryomyces hansenii HRB3 (Dh) on the bacterial community structure in reduced-salt dry sausage was investigated. The results demonstrated that the inoculation of two yeast strains significantly reduced the pH, and enhanced the total acid content, lactic acid bacteria (LAB) counts, and total bacterial counts of reduced-salt sausages after a 12-day fermentation (p < 0.05). Furthermore, high-throughput sequencing results elucidated that the inoculation of yeast strains significantly affected the bacterial composition of the dry sausages. Especially, the relative abundance of bacteria at the firmicute level in the Pk and Dh treatments exhibited a significant increase of 83.22% and 82.19%, respectively, compared to the noninoculated reduced-salt dry sausage treatment (Cr). The relative abundance of Latilactobacillus, especially L. sakei (0.46%, 2.80%, 65.88%, and 33.41% for the traditional dry sausage (Ct), Cr, Pk, and Dh treatments, respectively), increased significantly in the reduced-salt sausages inoculated with two yeast strains. Our work demonstrates the dynamic changes in the bacterial composition of reduced-salt sausages inoculated with different yeast strains, which could provide the foundation for the in-depth study of fungi-bacteria interactions in fermented foods.

Casein hydrolysate's effects on the fermentation properties, texture, and chemical characteristics and the bacterial microbiota of fermented glutinous rice dough.

To investigate how casein hydrolysate affected the physicochemical properties and microbiological diversity of the glutinous rice dough (natural fermentation and yeast fermentation), we analyzed its fermentation properties, carbohydrate, protein degradation, texture, and bacterial composition. According to the findings, casein hydrolysate increased the total LAB number, as well as organic acid content, in naturally fermented and yeast fermented glutinous rice dough by 3.59 and 8.19%, respectively, and reduced the fermentation time by at least 2 h. Meanwhile, casein hydrolysate enhanced the content of reducing sugars by 4.46 and 13.53% and increased protease activity by 29.9 and 27.7%. In addition, casein hydrolysate accelerated protein breakdown and regulated the hardness of the dough to improve the texture. Casein hydrolysate enriched the bacterial richness and diversity of dough. After adding casein hydrolysate, it promoted the growth of Pediococcus, Enterococcus, Lactobacillus, and Streptococcus. According to the Spearman correlation analysis, environmental factors (pH, lactic acid, acetic acid, reducing sugar content, and protease activity) exhibited the major driver for the abundance of bacterial species (Spearman correlation coefficient: -0.71 to 0.78). As a potential food additive, casein hydrolysate can improve the fermentation and quality of glutinous rice dough, increase consumer acceptance of cereal foods, and give consumers healthier options.

Characterization of the Bacterial Composition of 47 Fermented Foods in Sweden.

Fermentation has long been utilized to preserve and enhance the flavor and nutritional value of foods. Recently, fermented foods have gained popularity, reaching new consumer groups due to perceived health benefits. However, the microbial composition of many fermented foods re-mains unknown. Here, we characterized the bacterial composition, diversity, and richness of 47 fermented foods available in Sweden, including kombucha, water kefir, milk kefir, yogurt, plant-based yogurt alternatives, kimchi, sauerkraut, and fermented vegetables. Via 16S rRNA gene sequencing, we identified 2497 bacteria (amplicon sequence variants). The bacterial composition was strongly associated with the type of fermented food, and lactic acid bacteria and/or acetic acid bacteria dominated most samples. However, each fermented food had a unique composition, with kombucha and water kefir having the highest diversity across and within samples. Few bacteria were abundant in multiple foods and food groups. These were Streptococcus thermophilus in yogurts and plant-based yoghurts; Lactococcus lactis in milk kefirs and one water kefir; and Lactiplantibacillus plantarum in kimchi, sauerkraut, and fermented cucumber. The broad range of fermented foods included in this study and their diverse bacterial communities warrant further investigation into the implications of microbial compositions for product traits and potential impact on human health.

Different responses of abundant and rare bacterial composition to groundwater depth and reduced nitrogen application in summer maize field.

Introduction: It is well known that reduced nitrogen application and groundwater depth can change soil microbial communities, but the associated difference in the response of abundant and rare bacterial composition to these local environmental changes remains unclear. Methods: In this study a lysimeter experiment was carried out to examine the impact of reduced nitrogen and groundwater depth on the composition of abundant and rare bacteria. Results and discussion: Our results demonstrated that the summer maize field soil species composition of rare bacterial sub-communities was significantly regulated by reduced nitrogen application, groundwater depth change and their interactions. However, only reduced nitrogen application had a significant influence on the species composition of abundant bacterial sub-communities. The structural equation model (SEM) indicated that reduced nitrogen application and groundwater depth change also could indirectly regulate the species composition of abundant and rare bacteria by altering soil attributes. The changes in soil pH and TSN had the most significant effects on the community composition of abundant and rare bacteria, respectively. More importantly, rare bacterial sub-communities were more sensitive to the changes in nitrogen input, groundwater depth and soil factors. Collectively, our study first demonstrated that abundant and rare microbial sub-communities responded differently to reduced nitrogen application and groundwater depth change. This study highlights that summer maize farmland production management should take nitrogen input and groundwater depth into consideration to maintain the compositional stability of soil rare microbial sub-communities.

Distribution and co-occurrence networks of the bacterial community in sediment cores from the subtropical Daya Bay, China.

The bacterial community plays an important role in biogeochemical cycles in marine sediment. However, little is known about the vertical profiles and co-occurrence patterns of bacterial community in sediment cores from the marine environment. In this study, five sediment cores were taken from a subtropical bay in China, heavily impacted by anthropogenic activities. The bacterial composition in sediment cores was investigated by using high-throughput sequencing of the 16S rRNA gene. A principal coordinates analysis and an adonis analysis of the operational taxonomic unit (OTU) compositions showed that spatial variation, rather than vertical variation, determined the bacterial structure in sediment cores. The bacterial complexity varied greatly across the five sediment cores, and the rare taxa played an important role in supporting the stability of the bacterial network. This study revealed that sediment properties and anthropogenic activities may induce a shift in the bacterial composition in sediment cores of a subtropical bay.

Antibiotics and antibiotic resistance gene dynamics in the composting of antibiotic fermentation waste - A review.

Fate of antibiotics and antibiotic resistance genes (ARGs) during composting of antibiotic fermentation waste (AFW) is a major concern. This review article focuses on recent literature published on this subject. The key findings are that antibiotics can be removed effectively during AFW composting, with higher temperatures, appropriate bulking agents, and suitable pretreatments improving their degradation. ARGs dynamics during composting are related to bacteria and mobile genetic elements (MGEs). Higher temperatures, suitable bulking agents and an appropriate C/N ratio (30:1) lead to more efficient removal of ARGs/MGEs by shaping the bacterial composition. Keeping materials dry (moisture less than 30%) and maintaining pH stable around 7.5 after composting could inhibit the rebound of ARGs. Overall, safer utilization of AFW can be realized by optimizing composting conditions. However, further removal of antibiotics and ARGs at low levels, degradation mechanism of antibiotics, and spread mechanism of ARGs during AFW composting require further investigation.

Comprehensive analysis of the microbiome and metabolome in pus from pyogenic liver abscess patients with and without diabetes mellitus.

Introduction: Pyogenic liver abscess (PLA) patients combined with diabetes mellitus (DM) tend to have more severe clinical manifestations than without DM. The mechanism responsible for this phenomenon is not entirely clear. The current study therefore aimed to comprehensively analyze the microbiome composition and metabolome in pus from PLA patients with and without DM, to determine the potential reasons for these differences. Methods: Clinical data from 290 PLA patients were collected retrospectively. We analyzed the pus microbiota using 16S rDNA sequencing in 62 PLA patients. In addition, the pus metabolomes of 38 pus samples were characterized by untargeted metabolomics analysis. Correlation analyses of microbiota, metabolites and laboratory findings were performed to identify significant associations. Results: PLA patients with DM had more severe clinical manifestations than PLA patients without DM. There were 17 discriminating genera between the two groups at the genus level, among which Klebsiella was the most discriminating taxa. The ABC transporters was the most significant differential metabolic pathway predicted by PICRUSt2. Untargeted metabolomics analysis showed that concentrations of various metabolites were significantly different between the two groups and seven metabolites were enriched in the ABC transporters pathway. Phosphoric acid, taurine, and orthophosphate in the ABC transporters pathway were negatively correlated with the relative abundance of Klebsiella and the blood glucose level. Discussion: The results showed that the relative abundance of Klebsiella in the pus cavity of PLA patients with DM was higher than those without DM, accompanied by changes of various metabolites and metabolic pathways, which may be associated with more severe clinical manifestations.