The person-to-person transmission landscape of the gut and oral microbiomes.

The human microbiome is an integral component of the human body and a co-determinant of several health conditions1,2. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown3,4. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies5, especially those on non-infectious, microbiome-associated diseases.

Drought response revealed by chromatin organization variation and transcriptional regulation in cotton.

BACKGROUND: Cotton is a major world cash crop and an important source of natural fiber, oil, and protein. Drought stress is becoming a restrictive factor affecting cotton production. To facilitate the development of drought-tolerant cotton varieties, it is necessary to study the molecular mechanism of drought stress response by exploring key drought-resistant genes and related regulatory factors. RESULTS: In this study, two cotton varieties, ZY007 (drought-sensitive) and ZY168 (drought-tolerant), showing obvious phenotypic differences under drought stress, were selected. A total of 25,898 drought-induced genes were identified, exhibiting significant enrichment in pathways related to plant stress responses. Under drought induction, At subgenome expression bias was observed at the whole-genome level, which may be due to stronger inhibition of Dt subgenome expression. A gene co-expression module that was significantly associated with drought resistance was identified. About 90% of topologically associating domain (TAD) boundaries were stable, and 6613 TAD variation events were identified between the two varieties under drought. We identified 92 genes in ZY007 and 98 in ZY168 related to chromatin 3D structural variation and induced by drought stress. These genes are closely linked to the cotton response to drought stress through canonical hormone-responsive pathways, modulation of kinase and phosphatase activities, facilitation of calcium ion transport, and other related molecular mechanisms. CONCLUSIONS: These results lay a foundation for elucidating the molecular mechanism of the cotton drought response and provide important regulatory locus and gene resources for the future molecular breeding of drought-resistant cotton varieties.

Faecalibacterium prausnitzii Attenuates CKD via Butyrate-Renal GPR43 Axis.

BACKGROUND: Despite available clinical management strategies, chronic kidney disease (CKD) is associated with severe morbidity and mortality worldwide, which beckons new solutions. Host-microbial interactions with a depletion of Faecalibacterium prausnitzii in CKD are reported. However, the mechanisms about if and how F prausnitzii can be used as a probiotic to treat CKD remains unknown. METHODS: We evaluated the microbial compositions in 2 independent CKD populations for any potential probiotic. Next, we investigated if supplementation of such probiotic in a mouse CKD model can restore gut-renal homeostasis as monitored by its effects on suppression on renal inflammation, improvement in gut permeability and renal function. Last, we investigated the molecular mechanisms underlying the probiotic-induced beneficial outcomes. RESULTS: We observed significant depletion of Faecalibacterium in the patients with CKD in both Western (n=283) and Eastern populations (n=75). Supplementation of F prausnitzii to CKD mice reduced renal dysfunction, renal inflammation, and lowered the serum levels of various uremic toxins. These are coupled with improved gut microbial ecology and intestinal integrity. Moreover, we demonstrated that the beneficial effects in kidney induced by F prausnitzii-derived butyrate were through the GPR (G protein-coupled receptor)-43. CONCLUSIONS: Using a mouse CKD model, we uncovered a novel beneficial role of F prausnitzii in the restoration of renal function in CKD, which is, at least in part, attributed to the butyrate-mediated GPR-43 signaling in the kidney. Our study provides the necessary foundation to harness the therapeutic potential of F prausnitzii for ameliorating CKD.

Association of dexmedetomidine and intraoperative thermal insulation with postoperative outcomes in colorectal cancer resection.

OBJECTIVE: To investigate the effects of dexmedetomidine combined with intraoperative thermal insulation on postoperative cognitive function, cellular immune status and inflammatory markers in patients undergoing radical resection for colorectal cancer. METHODS: Fifty patients who underwent radical resection of colorectal cancer in our hospital from March 2020 to September 2021 were selected and divided into observation group (26 cases with dexmedetomidine combined with intraoperative thermal insulation intervention) and control group (24 cases with conventional anesthesia management). The evaluation measures included the mini-mental state scale (MMSE) score, CD4+ T cell, CD8+ T cell ratio and CD4+/CD8+ ratio, the level of inflammatory markers (IL-6, TNF-α, CRP), and the incidence of postoperative complications. RESULTS: The MMSE score of the observation group was significantly higher than that of the control group on the 3rd day after operation (p < 0.001). After treatment, the proportion of CD4+ T cells, the proportion of CD8+ T cells and the ratio of CD4+/CD8+ in observation group were higher than those in control group (p < 0.01), while the inflammatory markers IL-6, TNF-α and CRP were lower than those in control group (p < 0.01). The incidence of postoperative cognitive dysfunction (POCD) in the observation group (7.69%) was significantly lower than that in the control group (33.33%) (p = 0.010), and the postoperative infection rate was also significantly decreased (p = 0.042). CONCLUSION: Dexmedetomidine combined with intraoperative insulation can significantly improve postoperative cognitive function, maintain immune balance, reduce inflammatory response, and reduce the incidence of POCD and other postoperative complications in patients with radical resection of colorectal cancer.

The Synergistic Antimicrobial Effect and Mechanism of Nisin and Oxacillin against Methicillin-Resistant Staphylococcus aureus.

Methicillin-resistant Staphylococcus aureus (MRSA) is responsible for skin and soft tissue infections with multi-resistance to many antibiotics. It is thus imperative to explore alternative antimicrobial treatments to ensure future treatment options. Nisin (NIS), an antibacterial peptide produced by Lactococcus lactis, was selected to combine with Oxacillin (OX), to evaluate the antimicrobial effect and potential mechanism against MRSA. The synergistic antimicrobial effect of OX and NIS was verified by Minimal Inhibitory Concentration (MIC) assays, checkerboard analysis, time-kill curve, biofilm producing ability, and mice skin infection model in vivo. For the potential synergistic antimicrobial mechanism, the microstructure and integrity change of MRSA cells were determined by Scanning and Transmission Electron Microscope (SEM and TEM), intracellular alkaline phosphatase activity and propidium iodide staining were assayed; And transcription of mecA, main gene of MRSA resistant to OX, were detected by qRT-PCR. The results showed NIS could restore the sensitivity of MRSA to OX and inhibit biofilm production; OX + NIS can make MRSA cell deform; NIS may recover OX sensitivity by inhibiting the transcription of mecA. In vivo, mice skin infection models indicate that OX + NIS can substantially alleviate MRSA infections. As a safe commercially available biological compound, NIS and the combination of antibiotics are worth developing as new anti-MRSA biomaterials.

Bacteria-induced amino acid metabolism involved in appearance characteristics of high-temperature Daqu.

BACKGROUND: Significant changes occurd in Daqu bricks on the 15th day of incubation, and brick color (yellow, brown, or dark) is generally used as a standard for quality evaluation by experienced workers. This study aimed to explore the basis behind the phenomenon through multi-omics studies. The physicochemical properties of different high-temperature Daqu were compared. Furthermore, PacBio sequencing and the ultra-high-performance liquid chromatographic-Q-exactive-mass spectrometric approach were employed to analyze the differences in the microbiome and metabolome among different Daqu samples. RESULTS: Bacillus was the biomarker of yellow Daqu, Thermoactinomyces and Thermoascus were the key genera in brown Daqu, and Burkholderiales, Sphingomonas, and Ralstonia were biomarkers in dark Daqu. The physicochemical characteristics (especially the color values) of different high-temperature Daqu showed strong correlations with the bacterial alpha diversity and the relative abundance of dominant bacterial genera. Amino acid metabolism pathways including tryptophan metabolism, ß-alanine metabolism, and arginine biosynthesis were the key factors resulting in the characteristic differences where Bacillus, Burkholderia, Ralstonia, and Sphingomonas were pivotal bacterial genera. The relative abundance of Bacillus had a positive correlation with the content of 3-hydroxykynurenamine, l-glutamic acid, and pantothenic acid, while it showed a negative correlation with indoleacetic acid, l-tryptophan, N-acetylserotonin, l-histidine, l-aspartic acid, phosphatidylserine, 5-methoxyindoleacetate, and L-serine. Burkholderia, Ralstonia, and Sphingomonas had the opposite effects. CONCLUSION: Microbes play different roles in amino acid metabolism pathways, producing different metabolites, contributing to the differences in Daqu appearance and quality. © 2022 Society of Chemical Industry.

A Retrospective Study on the Effect of Empowerment Psychological Intervention Led by Specialist Nurses on Post-traumatic Stress Disorder in ICU Patients.

BACKGROUND: Many patients in the intensive care unit (ICU) suffer from post-traumatic stress disorder (PTSD), which seriously affects the treatment, recovery, and prognosis of patients. OBJECTIVE: To observe the effect of empowerment psychological intervention on the status of PTSD in ICU patients. METHODS: A total of 86 patients with PTSD who were treated in ICU from July 2019 to December 2021 were divided into two groups according to the intervention method. The control group (n = 43) used routine psychological intervention, while the intervention group (n = 43) used empowerment psychological intervention led by specialist nurses. The Pittsburgh Sleep Quality Index (PSQI) was used to assess the sleep quality of the patients. The Resilience Questionnaire (CD-RISC) was used to evaluate the resilience of the patients, and the Post Traumatic Stress Disorder Self-Rating Scale (PTSD-SS) was used to assess the severity of the symptoms. The Hamilton Anxiety and Depression Inventory (HAMA and HAMD) was adapted to assess the degree of anxiety and depression, and the Post-Traumatic Growth Inventory (PTGI) was adapted to evaluate the post-traumatic growth of the patients. RESULTS: After the intervention, the total CD-RISC score and its tenacity, self-improvement, and optimism scores in the two groups were all higher than before, and the total PSQI score and its sleep quality, time, efficiency and impairment, as well as hypnotic drugs, daytime dysfunction and time to sleep were lower than before, and the CD-RISC score in the intervention group was higher than that in the control group, PSQI score was lower than that in the control group (p < 0.05). After the intervention, PTSD-SS scores and anxiety-depression scores were lower, and PTGI scores were higher in both groups than before (p < 0.05). CONCLUSION: The empowerment psychological intervention led by specialist nurses applied to ICU patients with PTSD can improve their psychological resilience and sleep quality, reduce negative emotions, alleviate clinical symptoms, and promote post-traumatic growth.

Identifying psychiatric disorder-associated gut microbiota using microbiota-related gene set enrichment analysis.

Psychiatric disorders are a group of complex psychological syndromes with high prevalence. It has been reported that gut microbiota has a dominant influence on the risks of psychiatric disorders through gut microbiota-brain axis. We extended the classic gene set enrichment analysis (GSEA) approach to detect the association between gut microbiota and complex diseases using published genome-wide association study (GWAS) and GWAS of gut microbiota summary data. We applied our approach to real GWAS data sets of five psychiatric disorders, including attention deficiency/hyperactive disorder (ADHD), autism spectrum disorder (AUT), bipolar disorder (BD), schizophrenia (SCZ) and major depressive disorder (MDD). To evaluate the performance of our approach, we also tested the genetic correlations of obesity and type 2 diabetes with gut microbiota. We identified several significant associations between psychiatric disorders and gut microbiota, such as ADHD and genus Desulfovibrio (P = 0.031), order Clostridiales (P = 0.034). For AUT, association signals were observed for genera Bacteroides (P = 0.012) and Desulfovibrio (P = 0.033). Genus Desulfovibrio (P = 0.005) appeared to be associated with BD. For MDD, association signals were observed for genus Desulfovibrio (P = 0.003), order Clostridiales (P = 0.004), family Lachnospiraceae (P = 0.007) and genus Bacteroides (P = 0.007). Genus Desulfovibrio (P = 0.012) and genus Bacteroides (P = 0.038) appeared to be associated with SCZ. Our study results provide novel clues for revealing the roles of gut microbiota in psychiatric disorders. This study also illustrated the good performance of GSEA approach for exploring the relationships between gut microbiota and complex diseases.

Identification of vacuolar phosphate influx transporters in Brassica napus.

Recent progress has shown that vacuolar Pi transporters (VPTs) are important for cellular Pi homoeostasis in Arabidopsis thaliana and Oryza sativa under fluctuating external Pi supply, but the identity and involvement of VPTs in cellular Pi homoeostasis in Brassica napus is poorly understood. Here, we identified two vacuolar Pi influx transporters B. napus, BnA09PHT5;1b and BnCnPHT5;1b, and uncovered their necessity for cellular Pi homoeostasis through functional analysis. Both Brassica proteins are homologs of Arabidopsis AtPHT5;1 with a similar sequence, structure, tonoplast localization, and VPT activity. Brassica pht5;1b double mutants had smaller shoots and larger shoot cellular Pi concentrations than wild-type B. napus, which contrasts with a previous study of the Arabidopsis pht5;1 mutant, suggesting that PHT5;1-VPTs play different roles in cellular Pi homoeostasis in seedlings of B. napus and A. thaliana. Disruption of BnPHT5;1b genes also caused Pi toxicity in floral organs, reduced seed yield and impacted seed traits, consistent with the proposed role of AtPHT5;1 in floral Pi homoeostasis in Arabidopsis. Taken together, our studies identified two vacuolar Pi influx transporters in B. napus and revealed the distinct and conserved roles of BnPHT5;1bs in cellular Pi homoeostasis in this plant species.

Transcriptome and metabolome profiling of interspecific CSSLs reveals general and specific mechanisms of drought resistance in cotton.

In order to understand the molecular mechanism of cotton's response to drought during the flowering and boll stage, transcriptomics and metabolomics were carried out for two introgression lines (drought-tolerant line: T307; drought-sensitive line: S48) which were screened from Gossypium hirsutum cv. 'Emian22' with some gene fragments imported from Gossypium barbadense acc. 3-79, under drought stress by withdrawing water at flowering and boll stage. Results showed that the basic drought response in cotton included a series of broad-spectrum responses, such as amino acid synthesis, hormone (abscisic acid, ABA) signal transduction, and mitogen-activated protein kinases signal transduction pathway, which activated in both drought-tolerant and drought-sensitive lines. However, the difference of their imported fragments and diminished sequences triggers endoplasmic reticulum (ER) protein processing, photosynthetic-related pathways (in leaves), and membrane solute transport (in roots) in drought-tolerant line T307, while these are missed or not activated in drought-sensitive line S48, reflecting the different drought tolerance of the two genotypes. Virus-induced gene silencing assay of drought-tolerant differentially expressed heat shock protein (HSP) genes (mainly in leaf) and ATP-binding cassette (ABC) transporter genes (mainly in roots) indicated that those genes play important role in cotton drought tolerant. Combined analysis of transcriptomics and metabolomics highlighted the important roles of ER-stress-related HSP genes and root-specific ABC transporter genes in plants drought tolerance. These results provide new insights into the molecular mechanisms underlying the drought stress adaptation in cotton.

Variations of Personal Exposure to Particulate Nitrated Phenols from Heating Energy Renovation in China: The First Assessment on Associated Toxicological Impacts with Particle Size Distributions.

The clean heating renovation has been executed for improving particulate matter (PM) pollution in northern China since 2017. This study determined particle size distributions of nitrated phenols (NPs) in personal exposure samples and their associations with biomarkers in saliva and urine from homemakers in rural households of the Fenwei Plain, China. Remarkable reductions of 28.6-66.3% and 52.2-82.4% on PMs and total quantified NPs, respectively, were found with the substitutions of raw coal chunk and biomass by advanced clean coal. 4-Nitroguaiacol (4NG) showed the largest reductions of 81.2% among individual NP. In addition, the clean coal efficiently reduced interleukin-6 (IL-6) and 8-hydrox-2'-deoxyguanosine (8-OHdG) in the urine and saliva by 12-72%. Furthermore, significant positive correlations between urinary 8-OHdG with most of NPs in all particle sizes, urinary IL-6 with 4NG for particles with Dp > 2.5 µm and Dp = 0.25-1.0 µm and salivary IL-6 with 4-nitrocatechol and 4-methyl-5-nitrocatechol for particles with Dp > 2.5 µm, Dp = 0.5-1.0 µm, and Dp < 0.25 µm were observed but not for salivary 8-OHdG or PMs. The results provide scientific support for the clean energy reformation and demonstrate the strong particle size dependence between NPs and biomarkers.

Seasonal dynamics survey and association analysis of microbiota communities, antibiotic resistance genes distribution, and biotoxicities characterization in landfill-leachate.

OBJECTIVE: To reflect the potential and intrinsic association among microbiota structure, antibiotic resistance genes distribution and biological toxicity of landfill-leachate according to seasonal change, and accurately assess the potential threat of leachate to the surrounding environment. METHODS: On the basis of the leachate water quality monitoring data from January to December 2020, principal component analysis (PCA) was used to identify the main pollutants in the leachate; Vibrio fischeri luminescence inhibition test was used to detect the comprehensive biotoxicity of the leachate; 16S rDNA amplicon sequencing was used for leachate microbiota. q-PCR was used to detect the class 1 integron (intI1), and eight antibiotic resistance genes (sul1, sul2, tetA, tetB, tetM, tetQ, mefA, and mexF); Canonical correspondence (CCA) analysis was carried out for the association analysis. RESULT: The biotoxicity of leachate in the second quarter was the highest. The dominant phylum of leachate microbiota from 1st quarters to 4th quarters was Proteobacteria (94.97 %, 85.43 %, 88.20 %, and 84.11 %), and the dominant genera were Thiomonas (60.41 %, 26.83 %, 25.66 %, and 30.51 %), Pseudomonas (5.89 %, 1.86 %, 0.68 %, and 4.72 %), Desulfurella (8.52 %, 0.57 %, 3.81 %, and 8.25 %), and Acidithiobacillus (4.71 %, 0.69 %, 0.87 %, and 5.91 %); Nitrospirillum was negatively correlated with chemical oxygen demand (COD) (R=-0.561, P = 0.008) and five-day biochemical oxygen demand (BOD5) (R=-0.591, P = 0.005); Limnohabitans was positively correlated with pH (R=0.444, P = 0.044). Four AR genes (sul1, sul2，tetM, and tetQ) were detected in all the samples, while the second quarter had the highest concentration of sul1(6.31 ± 0.49 lg copies/ng DNA), tetM (3.01 ± 1.38 lg copies/ng DNA) and tetQ (3.64 ± 0.90 lg copies/ng DNA). CONCLUSION: As the mature landfill, the quality of this leachate met the pollution control standards for domestic waste landfills. Thiomycetes, Pseudomonas, Desulfurization, and Thiopterus acidophyllum constitute the dominant microbiota. However, leachate in the second quarter had more serious contamination, the higher biotoxicity, higher concentration of AR genes, together with higher microbiota richness and diversity, which deserved more attention for the potential threat to the surrounding environment.

Quantitative Proteomic Analysis Reveals the Key Molecular Events Driving Phaeocystis globosa Bloom and Dissipation.

Phaeocystis globosa is a marine-bloom-forming haptophyte with a polymorphic life cycle alternating between free-living cells and a colonial morphotype, that produces high biomass and impacts ecological structure and function. The mechanisms of P. globosa bloom formation have been extensively studied, and various environmental factors are believed to trigger these events. However, little is known about the intrinsic biological processes that drive the bloom process, and the mechanisms underlying P. globosa bloom formation remain enigmatic. Here, we investigated a P. globosa bloom occurring along the Chinese coast and compared the proteomes of in situ P. globosa colonies from bloom and dissipation phases using a tandem mass tag (TMT)-based quantitative proteomic approach. Among the 5540 proteins identified, 191 and 109 proteins displayed higher abundances in the bloom and dissipation phases, respectively. The levels of proteins involved in photosynthesis, pigment metabolism, nitrogen metabolism, and matrix substrate biosynthesis were distinctly different between these two phases. Ambient nitrate is a key trigger of P. globosa bloom formation, while the enhanced light harvest and multiple inorganic carbon-concentrating mechanisms support the prosperousness of colonies in the bloom phase. Additionally, colonies in the bloom phase have greater carbon fixation potential, with more carbon and energy being fixed and flowing toward the colonial matrix biosynthesis. Our study revealed the key biological processes underlying P. globosa blooms and provides new insights into the mechanisms behind bloom formation.

Integrated multi-omics approaches to understand microbiome assembly in Jiuqu, a mixed-culture starter.

The use of Jiuqu as a saccharifying and fermenting starter in the production of fermented foods is a very old biotechnological process that can be traced back to ancient times. Jiuqu harbors a hub of microbial communities, in which prokaryotes and eukaryotes cohabit, interact, and communicate. However, the spontaneous fermentation based on empirical processing hardly guarantees the stable assembly of the microbiome and a standardized quality of Jiuqu. This review describes the state of the art, limitations, and challenges towards the application of traditional and omics-based technology to study the Jiuqu microbiome and highlights the need for integrating meta-omics data. In addition, we review the varieties of Jiuqu and their production processes, with particular attention to factors shaping the microbiota of Jiuqu. Then, the potentials of integrated omics approaches used in Jiuqu research are examined in order to understand the assembly of the microbiome and improve the quality of the products. A variety of different approaches, including molecular and mass spectrometry-based techniques, have led to scientific advances in the analysis of the complex ecosystem of Jiuqu. To date, the extensive research on Jiuqu has mainly focused on the microbial community diversity, flavor profiles, and biochemical characteristics. An integrative approach to large-scale omics datasets and cultivated microbiota has great potential for understanding the interrelation of the Jiuqu microbiome. Further research on the Jiuqu microbiome may explain the inherent property of compositional stability and stable performance of a complex microbiota coping with environmental perturbations and provide important insights to reconstruct synthetic microbiota and develop modern intelligent manufacturing procedures for Jiuqu.

Microbial characteristics and metabolite profiles of high-temperature Daqu in different maturation stages.

The maturation period of high-temperature Daqu (HTD) is usually 3-6 months, and the characteristics of HTD at different maturation stages were different. In this study, the microbial characteristics and metabolite profiles of HTD at different maturation stages were revealed with the combination of physicochemical detection, the third generation Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) sequencing technology, gas chromatography-mass spectrometry (GC-MS), and gas chromatography-ion mobility spectrometry (GC-IMS). Results showed that HTD matured for 6 months (Mix_m6) had higher saccharification power but less culturable thermotolerant bacteria and fungi than HTD matured for 3 months (Mix_m3). The average relative abundances of Thermoactinomyces, Paenibacillus, and Rasamsonia in Mix_m3 were higher than that in Mix_m6, while the average relative abundances of Bacillus, Pseudomonas, Thermoascus increased obviously with the prolongation of the maturation period. Streptomyces and Thermoactinomyces were biomarkers in Mix_m3, while Burkholderia and Pseudomonas were regarded as biomarkers in Mix_m6. Differences in microbiota structure led to different enrichment of metabolic pathways in HTD at different maturation stages, resulting in different flavor profiles, especially in ethyl acetate, 1-octen-3-one, (E)-3-Hexen-1, 2,3,5-trimethy-6-ethylpyrazine, pyrazine, tetramethyl content. The microbiota and metabolite characteristics of HTD comprehensively reflected the HTD quality in different maturation stages, which provided a reference for determining the optimal maturation time.

Comparative study on inhibitory effects of ferulic acid and p-coumaric acid on Salmonella Enteritidis biofilm formation.

Biofilm cells exhibit higher resistance than their planktonic counterparts to commonly used disinfectants in food industry. Phenolic acids are promising substitute offering less selective pressure than traditional antibiotics. This study aims to evaluate the inhibitory effects of ferulic acid (FA) and p-coumaric acid (p-CA) on Salmonella Enteritidis biofilm formation and explore the underlying inhibitory mechanisms. The minimal inhibitory concentration (MIC) of FA and p-CA were 1.0 and 0.5 mg/ml, respectively. The sub-inhibitory concentration (1/8 MIC) significantly decreased biofilm formation without growth inhibitory effects. The biomass and extracellular polymeric substances (EPS) of S. Enteritidis biofilm as well as the bacterial swimming and chemotaxis abilities were significantly decreased when exposed to sub-MIC concentrations of FA and p-CA. These two phenolic acids showed high affinity to proteins involved in flagella motility and repressed the S. Enteritidis biofilm formation-related gene expressions. Furthermore, these two phenolic acids maintained high antibiofilm efficiency in simulated food processing conditions. This study provided valuable information of multiple phenotypic and molecular responses of S. Enteritidis to these two phenolic acids.

Characteristics of the microbiota and metabolic profile of high-temperature Daqu with different grades.

The superior grade Daqu (S_Daqu) and normal grade Daqu (N_Daqu) have obvious differences in flavor, fracture surface, appearance, etc., which can be accurately grouped by well-trained panel based on their sensory properties. However, the differences in microbial community diversity and metabolites between the S_Daqu and N_Daqu were still unclear. The culture-dependent method, the third generation Pacific Biosciences (PacBio) single-molecule, real-time (SMRT) sequencing technology, and nuclear magnetic resonance (NMR) were combined to show the characteristics in microorganisms and metabolites. Results showed that the fungal counts were higher in N_Daqu while the richness of bacterial communities was higher in S_Daqu (P < 0.05). Lentibacillus, Burkholderia, Saccharopolyspora, Thermoascus, and Rasamsonia were the dominant genera of S_Daqu while Staphylococcus, Scopulibacillus, and Chromocleista were the dominant genera in N_Daqu. The content of differential acids, amino acids, and alcohols including fumarate, glucuronate, glycine, 4-carboxyglutamate, and myo-inositol in S_Daqu was higher than that in N_Daqu by 1H NMR coupled with multivariate statistical analysis. The network analysis regarding microbes and metabolites suggested that Saccharopolyspora showed a strong positive correlation with 4-carboxyglutamate while Thermoascus and Chromocleista were highly negatively correlated with alanine and isobutyrate, respectively. Linear Discriminant Analysis (LDA) Effect Size (LEfSe) revealed that Macrococcus and Caulobacter were regarded as bacterial biomarkers in the S_Daqu while Chromocleista was the key fungal genera in N_Daqu. Functionality prediction indicated that the bacteria in S_Daqu were largely involved in more metabolic activities including biosynthesis, degradation, detoxification, and generation of precursor metabolite and energy.

A de novo 10q11.23q22.1 deletion detected by whole genome mate-pair sequencing: a case report.

BACKGROUND: Interstitial deletions of chromosome band 10q11-q22 was a genomic disorder distinguished by developmental delay, congenital cleft palate and muscular hypotonia. The phenotypes involved were heterogeneous, hinge on the variable breakpoints and size. CASE PRESENTATION: Here, we presented a patient with soft palate cleft, growth and development delay. The patient was a 2 years and 5 months girl who was not able to walk unless using a children's crutches to support herself. Whole-exome sequencing (WES) and whole-genome mate-pair sequencing (WGMS) were both performed by next generation sequencing (NGS). A 20.76 Mb deletion at 10q11.23q22.1 (seq[GRCh37/hg19]del(10)(50,319,387-71,083,899) × 1) was revealed by the WGMS, which was verified as de novo by quantitative polymerase chain reaction (QPCR). CONCLUSION: Children with 10q11-q22 deletions greater than 20 MB have never been reported before, and we are the first to report and provide a detailed clinical phenotype, which brings further knowledge of 10q11-q22 deletions.

Effects of domestic solid fuel combustion emissions on the biomarkers of homemakers in rural areas of the Fenwei Plain, China.

BACKGROUND: The health effects of heavy solid fuel use in winter in rural China are of concern. The effects of air pollution resulting from domestic solid fuel combustion in rural households on rural homemakers' biomarkers were revealed in this study. METHODS: In total, 75 female homemakers from rural areas of Guanzhong Basin, the Fenwei Plain, People's Republic of China, were randomly selected and divided into three groups (biomass users, coal users, and nonusers of solid fuel user [control group]). The differences in biological indicators, including 8-hydrox-2'-deoxyguanosine (8-OHdG), interlukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) in urine samples as well as blood pressure (BP, including systolic BP [SBP] and diastolic BP [DBP]) and heart rate (HR) among the groups in winter and summer were investigated using statistical analysis. RESULTS: IL-6, 8-OHdG, HR, SBP, and DBP were significantly higher in winter than in summer (P < 0.05) owing to the poor air quality resulted from the excessive use of solid fuels in winter. Significant seasonal differences in 8-OHdG were observed for both coal and biomass users. After the influence of confounders was removed, only IL-6 levels in the urine of solid fuel users were significantly higher than that of the control group. CONCLUSIONS: IL-6 is a sensitive biomarker representing inflammatory responses to particulate matter emitted through household solid fuel combustion. Locally, excessive use of solid fuels in winter posed serious PM2.5 pollution in this area and adverse effects on inflammatory biomarkers in these rural homemakers and induced DNA damage related to oxidative stress.

Effects of graded levels of starch on the non-specific immune responses, antioxidant capacities and intestinal health in Chinese mitten crab, Eriocheir inensis.

A 9-week feeding trial was conducted to investigate the effects of graded levels of dietary starch (12%, 17%, 22%, 27% and 32%) on growth, non-specific immune responses, antioxidant capacities, immunity genes expression levels and pathogen resistance in Chinese mitten crab, Eriocheir inensis (initial body weight: 10.5 ± 0.5 g). Results showed that the highest weight gain rate of crabs was obtained in group containing 22% dietary starch. The highest activity of acid phosphatase, phenoloxidase and lysozyme in blood was found in crabs fed with 22-27% dietary starch. Additionally, 17%-27% dietary starch significantly increased the activities of superoxide dismutase and glutathione peroxidase, reduced malondinaldehyde content and then increased the total antioxidant capacities in hepatopancreas of crabs. The highest activity of alanine aminotransferase and aspartate aminotransferase was found in crabs fed with 32% dietary starch, indicating that excess starch had a negative effect on the liver function of crabs. With the dietary starch level increased, the transcription factors gene expression of the pro-inflammatory factors were significantly up-regulated, and the highest ILF2, IL-16, Relish and ADAM10 was found in crabs fed with dietary 32% starch, which may potentially promote the inflammatory response in intestines. Moreover, with the dietary starch increased, the activity of phenoloxidase and lysozyme, as well as the gene expression of crustin, were all increased in crabs after challenge against Citrobacter freundii, which demonstrated that additional dietary starch could provide immune-protection and help crabs improve their resistance against pathogens. In conclusion, these results suggest that adequate dietary starch can increase growth, enhance innate immune responses and promote disease resistance, reduce oxidative stress and inflammatory response in E. inensis. Taken together, 22-27% dietary starch (25.9-30.8% dietary carbohydrate) was suggested as a digestible energy source in crabs feed.