Spatial distribution and assembly processes of bacterial communities in riverine and coastal ecosystems of a rapidly urbanizing megacity in China.

Rapid urbanization has precipitated significant anthropogenic pollution (nutrients and pathogens) in urban rivers and their receiving systems, which consequentially disrupted the compositions and assembly of bacterial community within these ecosystems. However, there remains scarce information regarding the composition and assembly of both planktonic and benthic bacterial communities as well as pathogen distribution in such environments. In this study, full-length 16S rRNA gene sequencing was conducted to investigate the bacterial community composition, interactions, and assembly processes as well as the distribution of potential pathogens along a riverine-coastal continuum in Shenzhen megacity, China. The results indicated that both riverine and coastal bacterial communities were predominantly composed of Gammaproteobacteria (24.8 ± 12.6 %), Alphaproteobacteria (16.1 ± 9.8 %), and Bacteroidota (14.3 ± 8.6 %), while sedimentary bacterial communities exhibited significantly higher diversity compared to their planktonic counterparts. Bacterial community patterns exhibited significant divergences across different habitats, and a significant distance-decay relationship of bacterial community similarity was particularly observed within the urban river ecosystem. Moreover, the urban river ecosystem displayed a more complex bacterial co-occurrence network than the coastal ecosystem, and a low ratio of negative:positive cohesion suggested the inherent instability of these networks. Homogeneous selection and dispersal limitation emerged as the predominant influences on planktonic and sedimentary bacterial communities, respectively. Pathogenic genera such as Vibrio, Bacteroides, and Acinetobacter, known for their roles in foodborne diseases or wound infection, were also identified. Collectively, these findings provided critical insights into bacterial community dynamics and their implications for ecosystem management and pathogen risk control in riverine and coastal environments impacted by rapid urbanization.

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.

Effects of chronic triclosan exposure on nephrotoxicity and gut microbiota dysbiosis in adult mice.

Triclosan (TCS), a broad-spectrum, lipophilic, and antibacterial agent, has been commonly used in cosmetics, medical devices, and household products. The toxicity of TCS has recently become a research hotspot. Emerging evidence has shown that TCS can easily migrate to humans and animals and cause adverse effects on various target organs. However, the effects of TCS exposure on nephrotoxicity and underlying mechanisms remain unknown. The aim of the present study was to explore TCS-induced nephrotoxicity. Therefore, we establish a mouse model based on adult male mice to explore the effects of 10-week TCS exposure (50 mg/kg) on kidney. After mice were sacrificed, their blood, feces, and renal tissues were harvested for further analysis. We found that TCS treatment dramatically caused kidney structural damage, and increased blood urea nitrogen (BUN) and creatinine (Cr) expression levels, which indicated renal dysfunction. In addition, TCS exposure increased the malondialdehyde (MDA) and decreased superoxide dismutase (SOD) and total cholesterol (TCHO) expression levels, which indicated oxidative stress and lipid metabolism changes. The RNA sequencing (RNA-seq) of kidney tissue identified 221 differentially expressed genes (DEGs) enriched in 50 pathways, including drug metabolism-other enzymes, oxidative phosphorylation, glutathione metabolism, and inflammatory mediator regulation of TRP channels signaling pathways. The full-length 16S rRNA gene sequencing results showed that TCS exposure altered the community of gut microbiota, which was closely related to renal function damage. The above findings provide new insights into the mechanism of TCS-induced nephrotoxicity.

The rotation of primary starter culture mixtures results in batch-to-batch variations during Gouda cheese production.

Industrial production of Gouda cheeses mostly relies on a rotated use of different mixed-strain lactic acid bacteria starter cultures to avoid phage infections. However, it is unknown how the application of these different starter culture mixtures affect the organoleptic properties of the final cheeses. Therefore, the present study assessed the impact of three different starter culture mixtures on the batch-to-batch variations among Gouda cheeses from 23 different batch productions in the same dairy company. Both the cores and rinds of all these cheeses were investigated after 36, 45, 75, and 100 weeks of ripening by metagenetics based on high-throughput full-length 16S rRNA gene sequencing accompanied with an amplicon sequence variant (ASV) approach as well as metabolite target analysis of non-volatile and volatile organic compounds. Up to 75 weeks of ripening, the acidifying Lactococcus cremoris and Lactococcus lactis were the most abundant bacterial species in the cheese cores. The relative abundance of Leuconostoc pseudomesenteroides was significantly different for each starter culture mixture. This impacted the concentrations of some key metabolites, such as acetoin produced from citrate, and the relative abundance of non-starter lactic acid bacteria (NSLAB). Cheeses with the least Leuc. pseudomesenteroides contained more NSLAB, such as Lacticaseibacillus paracasei that was taken over by Tetragenococcus halophilus and Loigolactobacillus rennini upon ripening time. Taken together, the results indicated a minor role of leuconostocs in aroma formation but a major impact on the growth of NSLAB. The relative abundance of T. halophilus (high) and Loil. rennini (low) increased with ripening time from rind to core. Two main ASV clusters of T. halophilus could be distinguished, which were differently correlated with some metabolites, both beneficial (regarding aroma formation) and undesirable ones (biogenic amines). A well-chosen T. halophilus strain could be a candidate adjunct culture for Gouda cheese production.

Evaluation of stirring time through a rumen simulation technique: Influences on rumen fermentation and bacterial community.

Introduction: Rumen motility is a key element that influences ruminant nutrition, whereas little is known about the effects of rumen contraction duration on rumen fermentation and ruminal microbiome. We previously reported that proper rotation speed of a rumen simulation technique (RUSITEC) system enhanced rumen fermentation and microbial protein (MCP) production. In the present study, different contraction durations and intervals were simulated by setting different stirring times and intervals of the stirrers in a RUSITEC system. The objective of this trial was to evaluate the influences of stirring time on rumen fermentation characteristics, nutrient degradation, and ruminal bacterial microbiota in vitro. Methods: This experiment was performed in a 3 × 3 Latin square design, with each experimental period comprising 4 d for adjustment and 3 d for sample collection. Three stirring time treatments were set: the constant stir (CS), the intermittent stir 1 (each stir for 5 min with an interval of 2 min, IS1), and the intermittent stir 2 (each stir for 4 min with an interval of 3 min, IS2). Results: The total volatile fatty acid (TVFA) concentration, valerate molar proportion, ammonia nitrogen level, MCP density, protozoa count, disappearance rates of dry matter, organic matter, crude protein, neutral detergent fiber, and acid detergent fiber, emissions of total gas and methane, and the richness index Chao 1 for the bacterial community were higher (p < 0.05) in the IS1 when compared to those in the CS. The greatest TVFA, MCP, protozoa count, nutrient disappearance rates, gas productions, and bacterial richness indices of Ace and Chao 1 amongst all treatments were observed in the IS2. The relative abundance of the genus Treponema was enriched (p < 0.05) in CS, while the enrichment (p < 0.05) of Agathobacter ruminis and another two less known bacterial genera were identified in IS2. Discussion: It could be concluded that the proper reduction in the stirring time might help to enhance the feed fermentation, MCP synthesis, gas production, and the relative abundances of specific bacterial taxa.

Bacterial community structure and metabolic activity of drinking water pipelines in buildings: A new perspective on dual effects of hydrodynamic stagnation and algal organic matter invasion.

Eutrophication and algal blooms have become global issues. The drinking water treatment process suffers from pollution by algal organic matter (AOM) through cell lysis during the algal blooms. Nevertheless, it remains unclear how AOM invasion affects water quality and microbial communities in drinking water, particularly in the stagnant settings. In this study, the addition of AOM caused the residual chlorine to rapidly degrade and below the limit of 0.05 mg/L, while the NO2--N concentration ranged from 0.11 to 3.71 mg/L. Additionally, total bacterial counts increased and subsequently decreased. The results of Biolog demonstrated that the AOM significantly improved the utilization capacity of carbon sources and changed the preference for carbon sources. Full-length 16S rRNA gene sequencing and network modeling revealed a considerable reduction in the abundance of Proteobacteria, whereas that of Bacteroidetes increased significantly under the influence of AOM. Furthermore, the species abundance distributions of the Microcystis group and Scenedesmus group was most consistent with the Mandelbrot model. According to redundancy analysis and structural equation modeling, the bacterial community structure of the control group was most positively regulated by the free residual chlorine concentrations, whereas the Microcystis group and Scenedesmus group were positively correlated with the total organic carbon (TOC) concentration. Overall, these findings provide a scientific foundation for the evolution of drinking water quality under algae bloom pollution.

Stagnation trigger changes to tap water quality in winter season: Novel insights into bacterial community activity and composition.

The drinking water distribution system is important for water supply and it affects the quality of the drinking water. Indoor pipeline water quality is regulated by physical, hydraulic and biological elements, such as indoor temperature and stagnation. In this work, the effects of indoor heating and overnight stagnation on the variation in bacterial community structure and the total cell count were assessed by full-length 16S rRNA gene sequencing and flow cytometry, respectively. The results exhibited that the average intact cell count was 6.99 × 104 cells/mL and the low nucleic acid (LNA) bacteria was 4.48 × 104 cells/mL after stagnation. The average concentration of total and intracellular adenosine triphosphate (ATP) was 3.64 × 10-12 gATP/mL and 3.13 × 10-17 gATP/cell in stagnant water, respectively. The growth of LNA cells played a crucial role in increasing ATP. The dominant phylum observed was Proteobacteria (87.21 %), followed by Actinobacteria (8.25 %). Opportunistic pathogens increased the risk of disease in stagnant water (up to 1.2-fold for Pseudomonas sp. and 5.8-fold for Mycobacterium sp.). Meanwhile, structural equation model (SEM) and redundancy analysis (RDA) also illustrated that water temperature, residual chlorine and Fe significantly affected the abundance and composition of bacterial community. Taking together, these results show response of tap water quality to overnight stagnation and indoor heating, and provide scientific basis for drinking water security management in winter season.

Characterization of gut microbiota based on full-length 16S rRNA gene sequencing in high diamine oxidase population / 中华微生物学和免疫学杂志

Objective:To investigate the correlation between gut microbiota and serum diamine oxidase (DAO) level and to analyze the differences in gut microbiota between high DAO (DAO-H) and normal DAO populations.Methods:This study recruited 62 adult volunteers (31 in DAO-H group and 31 in normal control group) taking health examination in the Strategic Support Forces Special Medical Center in 2021. Their stool samples were collected to analyze the composition of gut microbiota in the two populations by full-length 16S rRNA gene sequencing.Results:No significant difference in the alpha diversity of gut microbiota was found between the DAO-H group and the normal control group, but the structure and function of gut microbiota varied. In the DAO-H group, commensal bacteria decreased, such as Phocaeicola and Bacteroidetes, while potential pathogenic bacteria increased, such as Klebsiella pneumoniae. There were changes in the metabolism of gut microbiota in the DAO-H group, including inhibited sphingolipid metabolism and enhanced biosynthesis of vancomycin group antibiotics, one carbon pool by folate pathway, terpenoid backbone biosynthesis, cell cycle-Caulobacter, protein export, base excision repair and nitrogen metabolism.Conclusions:Compared with the people with normal DAO, the population with high DAO had unique characteristics in gut microbiota composition and metabolism.

Potential Roles of the Free Salivary Microbiome Dysbiosis in Periodontal Diseases.

Saliva is a vital mediator in the oral cavity. The dysbiosis of free bacteria in saliva might be related to the onset, development, prognosis, and recurrence of periodontal diseases, but this potential relationship is still unclear. The objective of this study was to investigate the potential roles of the free salivary microbiome in different periodontal statuses, their reaction to nonsurgical periodontal therapy, and differences between diseased individuals after treatment and healthy persons. We recruited 15 healthy individuals, 15 individuals with gingivitis, and 15 individuals with stage I/II generalized periodontitis. A total of 90 unstimulated whole saliva samples were collected and sequenced using full-length bacterial 16S rRNA gene sequencing. We found that as the severity of disease increased, from healthy to gingivitis and periodontitis, the degree of dysbiosis also increased. A higher abundance of Prevotella intermedia and Catonella morbi and a lower abundance of Porphyromonas pasteri, Prevotella nanceiensis, and Haemophilus parainfluenzae might be biomarkers of periodontitis, with an area under curve (AUC) reaching 0.9733. When patients received supragingival scaling, there were more pathogens related to recolonization in the saliva of periodontitis patients than in healthy persons. Even after effective nonsurgical periodontal therapy, individuals with periodontitis displayed a more dysbiotic and pathogenic microbial community in their saliva than healthy individuals. Therefore, the gradual transition in the entire salivary microbial community from healthy to diseased includes a gradual shift to dysbiosis. Free salivary pathogens might play an important role in the recolonization of bacteria as well as the prognosis and recurrence of periodontal diseases.

DNA extraction method influences human milk bacterial profiles.

AIMS: To evaluate four DNA extraction methods to elucidate the most effective method for bacterial DNA recovery from human milk (HM). METHODS AND RESULTS: Human milk DNA was extracted using the following methods: (i) Qiagen MagAttract Microbial DNA Isolation Kit (kit QM), (ii) Norgen Milk Bacterial DNA Isolation Kit (kit NM), (iii) Qiagen MagAttract Microbiome DNA/RNA Isolation Kit (kit MM) and (iv) TRIzol LS Reagent (method LS). The full-length 16S rRNA gene was sequenced. Kits MM and method LS were unable to extract detectable levels of DNA in 9/11 samples. Detectable levels of DNA were recovered from all samples using kits NM (mean = 0·68 ng µl-1 ) and QM (mean = 0·55 ng µl-1 ). For kits NM and QM, the greatest number of reads were associated with Staphylococcus epidermidis, Streptococcus vestibularis, Propionibacterium acnes, Veillonella dispar and Rothia mucilaginosa. Contamination profiles varied substantially between kits, with one bacterial species detected in negative extraction controls generated with kit QM and six with kit NM. CONCLUSIONS: Kit QM is the most suitable of the kits tested for the extraction of bacterial DNA from human milk. SIGNIFICANCE AND IMPACT OF THE STUDY: Choice of extraction method impacts the efficiency of bacterial DNA extraction from human milk and the resultant bacterial community profiles generated from these samples.