Few studies have described the key features and prognostic roles of lung microbiota in patients with severe community-acquired pneumonia (SCAP). We prospectively enrolled consecutive SCAP patients admitted to ICU. Bronchoscopy was performed at bedside within 48 h of ICU admission, and 16S rRNA gene sequencing was applied to the collected bronchoalveolar lavage fluid. The primary outcome was clinical improvements defined as a decrease of 2 categories and above on a 7-category ordinal scale within 14 days following bronchoscopy. Sixty-seven patients were included. Multivariable permutational multivariate analysis of variance found that positive bacteria lab test results had the strongest independent association with lung microbiota (R² = 0.033; P = 0.018), followed by acute kidney injury (AKI; R² = 0.032; P = 0.011) and plasma MIP-1β level (R² = 0.027; P = 0.044). Random forest identified that the families Prevotellaceae, Moraxellaceae, and Staphylococcaceae were the biomarkers related to the positive bacteria lab test results. Multivariable Cox regression showed that the increase in α-diversity and the abundance of the families Prevotellaceae and Actinomycetaceae were associated with clinical improvements. The positive bacteria lab test results, AKI, and plasma MIP-1β level were associated with patients' lung microbiota composition on ICU admission. The families Prevotellaceae and Actinomycetaceae on admission predicted clinical improvements.
Acute Kidney Injury/complications* ; Bacteria/classification* ; Chemokine CCL4/blood* ; Community-Acquired Infections/microbiology* ; Humans ; Lung ; Microbiota/genetics* ; Pneumonia, Bacterial/diagnosis* ; Prognosis ; RNA, Ribosomal, 16S/genetics*

Clostridia inhabiting in jiupei and pit mud plays key roles in the formation of flavour during the fermentation process of Luzhou-flavour baijiu. However, the differences of Clostridial communities between jiupei and pit mud remains unclear. Here, the species assembly, succession, and metabolic capacity of Clostridial communities between jiupei and pit mud were analysed by high-throughput sequencing and pure culture approaches. The ratio of Clostridial biomass to bacterial biomass in the pit mud was relatively stable (71.5%-91.2%) throughout the fermentation process. However, it varied widely in jiupei (0.9%-36.5%). The dominant Clostridial bacteria in jiupei were Clostridium (19.9%), Sedimentibacter (8.8%), and Hydrogenispora (7.2%), while Hydrogenispora (57.2%), Sedimentibacter (5.4%), and Caproiciproducens (4.9%) dominated in the Clostridial communities in pit mud. The structures of Clostridial community in pit mud and jiupei were significantly different (P=0.001) throughout fermentation. Isolated Clostridial strains showed different metabolic capacities of volatile fatty acids in pure culture. Spatial and temporal heterogeneity of Clostridial communities existed in the baijiu fermentation pit, which was closely related to the main flavour components of Luzhou-flavour baijiu.
Alcoholic Beverages ; microbiology ; Bacteria ; classification ; metabolism ; Clostridium ; physiology ; Fatty Acids, Volatile ; metabolism ; Fermentation ; Food Microbiology

This study is to explore the effect of Qingfei Paidu Decoction(QPD) on the host metabolism and gut microbiome of rats with metabolomics and 16 S rDNA sequencing. Based on 16 S rDNA sequencing of gut microbiome and metabolomics(GC-MS and LC-MS/MS), we systematically studied the serum metabolites profile and gut microbiota composition of rats treated with QPD for continued 5 days by oral gavage. A total of 23 and 43 differential metabolites were identified based on QPD with GC-MS and LC-MS/MS, respectively. The involved metabolic pathways of these differential metabolites included glycerophospholipid metabolism, linoleic acid metabolism, TCA cycle and pyruvate metabolism. Meanwhile, we found that QPD significantly regulated the composition of gut microbiota in rats, such as enriched Romboutsia, Turicibacter, and Clostridium_sensu_stricto_1, and decreased norank_f_Lachnospiraceae. Our current study indicated that short-term intervention of QPD could significantly regulate the host metabolism and gut microbiota composition of rats dose-dependently, suggesting that the clinical efficacy of QPD may be related with the regulation on host metabolism and gut microbiome.
Animals ; Bacteria ; classification ; Chromatography, Liquid ; Drugs, Chinese Herbal ; pharmacology ; Gastrointestinal Microbiome ; drug effects ; Metabolomics ; Rats ; Tandem Mass Spectrometry

OBJECTIVE: To investigate changes in intestinal flora in patients with primary Sj?gren syndrome (pSS) and explore the relationship between pSS disease activity and intestinal flora structure. METHODS: Fecal samples were collected from 18 female pSS patients, including 9 patients with active disease (group A) and 9 with disease inactivity or low activity (group B), with 10 healthy subjects as the control group. The total bacterial DNA was extracted from the fecal samples for PCR amplification, and Illumina Hiseq 2500 high-throughput sequencing was performed for the v3-v4 region of 16Sr DNA gene to obtain the biological information of the intestinal flora. The intergroup OTU analysis, structural diversity analysis, significant difference analysis and LEFSE analysis were performed with information mining of the literature think tanks. RESULTS: The dilution curves generated based on the OTUshannon index for analysis of sample complexity showed that the measured data were relatively complete and could reflect the diversity of the microorganisms in the subjects. Analysis of the Alpha diversity index showed that the Shannon index differed significantly between group A and group B, and the Simpson index differed significantly between group A and group B and between group A and the control group ( < 0.05). Sequence analysis the 3 groups all consisted mainly of 4 phylum (, , , showed that the intestinal flora in and ) and 4 genera (, , , and ), all showing no significant differences among the 3 groups ( > 0.05) with the exception of genus, which differed significantly among the 3 groups ( < 0.05). The 16S v3-v4 region in the genus , , , , , , , , , , -, and differed significantly among the 3 groups ( < 0.05). The high-dimensional biometrics and genomic characteristics of the intestinal microorganisms differed significantly among the 3 groups ( < 0.05). According to the size of LDA SCORE (effect size), the core flora in group A included the genera , , -, , -, , , , and , as compared with the genera , , , , , -, , - and in the control group. CONCLUSIONS Patients with pSS have significant changes in the diversity of intestinal flora, especially in some specific bacteria in genus and in 16S v3-v4 region of the bacteria. The differences in the core bacteria in the intestinal flora of pSS patients suggest the role of flora structure changes in the pathogenesis of pSS.
Bacteria ; classification ; genetics ; Biodiversity ; DNA, Bacterial ; genetics ; Feces ; microbiology ; Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S ; genetics ; Sjogren's Syndrome ; microbiology

Objective: High PM concentration is the main feature of increasing haze in developing states, but information on its microbial composition remains very limited. This study aimed to determine the composition of microbiota in PM in Guangzhou, a city located in the tropics in China. Methods: In Guangzhou, from March 5 to 10 , 2016, PM was collected in middle volume air samplers for 23 h daily. The 16S rDNA V4 region of the PM sample extracted DNA was investigated using high-throughput sequence. Results: Among the Guangzhou samples, , , , , and were the dominant microbiota accounting for more than 90% of the total microbiota, and was the dominant gram-negative bacteria, accounting for 21.30%-23.57%. We examined the difference in bacterial distribution of PM between Beijing and Guangzhou at the genus level; was found in both studies, but was only detected in Guangzhou. Conclusion In conclusion, the diversity and specificity of microbial components in Guangzhou PM were studied, which may provide a basis for future pathogenicity research in the tropics.
Air Microbiology ; Air Pollutants ; analysis ; Bacteria ; classification ; isolation & purification ; China ; Cities ; Environmental Monitoring ; Microbiota ; Particle Size ; Particulate Matter ; analysis ; RNA, Bacterial ; analysis ; RNA, Ribosomal, 16S ; analysis

Objective To investigate the correlation between serum total 25-hydroxyvitamin D[T-25(OH)D]level and fecal microbiota in patients with inflammatory bowel disease(IBD). Methods Twenty-three patients with IBD completed the tests for serum T-25(OH)D,and the fecal microbiota was studied using V4 hypervariable region of 16S ribosomal RNA(rRNA)gene sequencing.According to serum T-25(OH)D level,the patients were divided into three groups including vitamin D normal group(
Bacteria/classification* ; Feces/microbiology* ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/microbiology* ; RNA, Ribosomal, 16S/genetics* ; Vitamin D/blood*

This study was designed to investigate the effect of Gegen Qinlian(GGQL) Decoction and its different compatibility groups on gut microbiota in rats with acute enteritis, and to explore the efficacy of GGQL Decoction in improving acute enteritis and gut microbiota. Male SD rats were randomly divided into control group, model group, positive control group(SASP), GGQL decoction group, Glycyrrhizae-free group(QGC), Puerariae-free group(QGG), Qinlian-free group(QQL), and Qinlian group(QL). The pathological sections and detection indexes of the rats were observed before and after modeling and administration. After 7 days of administration, fecal samples from 24 rats were collected and Illumina Miseq platform was used for high-throughput sequencing. From the anti-inflammatory and pharmacodynamic indicators, the effect was the most obvious in GGQL Decoction group, QGC group, QGG group and QL group(P<0.05). The alpha diversity and beta diversity showed that there were significant differences in the composition of intestinal flora in each group. As compared with the model group, the increased abundance and diversity of the flora caused by acute inflammation could be down-regulated in all groups except QQL group(P<0.05). The differential bacteria were explored by using LEfSe analysis, and the results showed that Bifidobacterium and other beneficial bacteria only appeared in the normal group. As compared with the normal group, Lactobacillus was significantly reduced(P<0.01), and Bacteroides, Flavonifractor and Clostridium_sensu_stricto_1 were up-regulated in model group(P<0.05, P<0.01). As compared with the model group, the number of Akkermansia was significantly increased(P<0.05), and the number of Clostridium_sensu_stricto_1 associated with intestinal inflammatory diseases was decreased in the GGQL Decoction group, QGC group and QL group. QGC group and QQL group caused the up-regulation of Ruminococcaceae and induced enrichment of Desulfovibrio which could lead to colon cell toxicity; QGG group caused the up-regulation of Proteobacteria and Burkhonderiales. The study suggests that the GGQL Decoction may play a role in the treatment of acute enteritis partially through improving the intestinal barrier, regulating the immune response and the structure of gut microbiota.
Animals ; Bacteria/classification* ; Drugs, Chinese Herbal/pharmacology* ; Enteritis/drug therapy* ; Feces ; Gastrointestinal Microbiome/drug effects* ; High-Throughput Nucleotide Sequencing ; Male ; Random Allocation ; Rats ; Rats, Sprague-Dawley

Gastrodia elata is a heterotrophic plant that needed to be symbiotic with Armillaria. The obstacle of continuous cropping in G. elata is serious during the G. elata cultivation, and the mechanism of obstacle in G. elata continuous cropping had not been solved. The planting of G. elata-Phallus impudicus is a new sequential planting pattern adopted in Guizhou province, but the effect of the cultivation on soil microbial community structure is still unclear. In this study, we collected four soil samples for the research including the soil without planted G. elata as control(CK), rhizosphere soil samples tightly adhering to the G. elata surface(GE), rhizosphere soil samples tightly adhering to Armillaria which was symbiotic with G. elata(AGE), the rhizosphere soil of P. impudicus planting after G. elata cultivation(PI). In order to explore the mechanism, the research study on the soil of G. elata-P. impudicus by using ITS and 16 S rDNA high-throughput sequencing technologies to detect soil microbial community structure including fungi and bacteria in the soil of CK, AGE, GE and PI. OTU clustering and PCA analysis of soil samples showed that the soil microbial diversity was relatively similar in AGE and GE. And the soil microbial in PI and CK clustered together. The results showed that AGE and GE had similar soil microbial diversity, as well as PI and CK. Compared with CK, the soil microbial diversity and abundance in AGE and GE were significantly increased. But the microbial diversity and abundance decreased in PI compared with AGE and GE. The annotation indicated that the abundance of Basidiomycota, Acidobacteria and Chloroflexi decreased, and that of Ascomycota, Zygomycota and Proteobacteria increased in AGE and GE compared with CK. In contrast to AGE and GE, PI was the opposite. The abundance of Basidiomycota, Acidobacteria and Chloroflexi increased in PI compared with AGE and GE. The abundance of microorganisms in the soil of PI and CK was similar. In addition, the co-culture of Armillaria and P. impudicus indicated that P. impudicus had obvious antagonistic effects on the growth of Armillaria. Therefore, it is speculated that the mechanism of G. elata-P. impudicus planting pattern related to the change of soil microbial. And we supposed that P. impudicus might inhibit the growth of Armillaria and change the soil microbial community structure and the abundance of soil microbial. And the soil microbial community structure was restored to a state close to that of uncultivated G. elata. Thus, the structure of soil microbial community planting G. elata could be restored by P. impudicus planting.
Agaricales/growth & development* ; Bacteria/classification* ; Fungi/classification* ; Gastrodia/microbiology* ; Microbiota ; Rhizosphere ; Soil Microbiology

OBJECTIVES: The emergence of resistant bacteria is being increasingly reported around the world, potentially threatening millions of lives. Amongst resistant bacteria, methicillin-resistant Staphylococcus aureus (MRSA) is the most challenging to treat. This is due to emergent MRSA strains and less effective traditional antibiotic therapies to Staphylococcal infections. The use of bacteriophages (phages) against MRSA is a new, potential alternate therapy. In this study, morphology, genetic and protein structure of lytic phages against MRSA have been analysed. METHODS: Isolation of livestock and sewage bacteriophages were performed using 0.4 μm membrane filters. Plaque assays were used to determine phage quantification by double layer agar method. Pure plaques were then amplified for further characterization. Sulfate-polyacrylamide gel electrophoresis and random amplification of polymorphic DNA were run for protein evaluation, and genotyping respectively. Transmission electron microscope was also used to detect the structure and taxonomic classification of phage visually. RESULTS: Head and tail morphology of bacteriophages against MRSA were identified by transmission electron microscopy and assigned to the Siphoviridae family and the Caudovirales order. CONCLUSION: Bacteriophages are the most abundant microorganism on Earth and coexist with the bacterial population. They can destroy bacterial cells successfully and effectively. They cannot enter mammalian cells which saves the eukaryotic cells from lytic phage activity. In conclusion, phage therapy may have many potential applications in microbiology and human medicine with no side effect on eukaryotic cells.
Agar ; Bacteria ; Bacteriophages ; Caudovirales ; Classification ; DNA ; Electrophoresis ; Eukaryotic Cells ; Head ; Humans ; Livestock ; Membranes ; Methicillin Resistance ; Methicillin-Resistant Staphylococcus aureus ; Methods ; Microscopy, Electron, Scanning Transmission ; Microscopy, Electron, Transmission ; Sewage ; Siphoviridae ; Staphylococcal Infections ; Tail

Mammary lesions in sows can prevent suckling piglets from consuming colostrum that provides fundamental nutrients and protective immunity. Although mammary gross lesions are frequently found in sows at farms or slaughterhouses, with the exception of mastitis, they have received little research attention. In this study, we investigated mammary lesions observed in South Korean sows between 2015 and 2016. Mammary tissue samples of 82 sows showing gross lesions during meat inspection were histologically classified and immunohistochemical analysis was conducted to assess the expression of estrogen receptor (ER)-α, ER-β, and progesterone receptor (PR) for mammary hyperplastic lesions as well as that of cluster of differentiation (CD) 3, CD79a, interleukin (IL)-1α, IL-1β, IL-6, and IL-8 for mastitis. Furthermore, 20 swab samples were cultured, and the isolated bacteria were identified using polymerase chain reactions for 16S ribosomal RNA genes. The lesions were classified as hyperplasia, mastitis, or hyperplasia with mastitis. Immunohistochemistry results revealed that there was neither expression of ER-α nor of ER-β, but all examined hyperplastic samples expressed PR. In addition, there was a significant correlation between CD3 and IL-1β expressions, as well as between IL-1β and IL-6 expressions. Regarding the identity of the isolated bacteria, Pseudomonas spp. were most frequently detected. The results of this study have revealed the incidence and characteristics of porcine mammary lesions.
Abattoirs ; Agriculture ; Bacteria ; Bacterial Infections ; Classification ; Colostrum ; Cytokines ; Estrogens ; Female ; Hyperplasia ; Immunohistochemistry ; Incidence ; Interleukin-6 ; Interleukin-8 ; Interleukins ; Mammary Glands, Human ; Mastitis ; Meat ; Polymerase Chain Reaction ; Pseudomonas ; Receptors, Progesterone ; RNA, Ribosomal, 16S ; Swine