The human microbiome harbors a diverse array of microbes which establishes a mutually beneficial relation with the host in healthy conditions, however, the dynamic homeostasis is influenced by both host and environmental factors. Smoking contributes to modifications of the oral, lung and gut microbiome, leading to various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn’s disease, ulcerative colitis and cancers. However, the exact causal relationship between smoking and microbiome alteration remains to be further explored.

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High throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues to rely on cumbersome journal publications for the description of new species, which still constitute the smallest taxonomic units. In response, we introduce LINbase, a web server that allows users to genomically circumscribe any group of prokaryotes with measurable DNA similarity and that uses the individual isolate as smallest unit. Since LINbase leverages the concept of Life Identification Numbers (LINs), which are codes assigned to individual genomes based on reciprocal average nucleotide identity, we refer to groups circumscribed in LINbase as LINgroups. Users can associate with each LINgroup a name, a short description, and a URL to a peer-reviewed publication. As soon as a LINgroup is circumscribed, any user can immediately identify query genomes as members and submit comments about the LINgroup. Most genomes currently in LINbase were imported from GenBank, but users can upload their own genome sequences as well. In conclusion, LINbase combines the resolution of LINs with the power of crowdsourcing in support of a highly resolved, genome phylogeny-based digital taxonomy. LINbase is available at http://www.LINbase.org.

Background: To examine the influence of positive end-expiratory pressure (PEEP) settings on lung mechanics and oxygenation in elderly patients undergoing thoracoscopic surgery.Methods: One hundred patients aged >65 years were randomly allocated into either the PEEP 5 or the electrical impedance tomography (EIT) group (PEEP EIT ). Each group underwent volume-controlled ventilation (tidal volume 6 mL/kg predicted body weight) with the PEEP either fixed at 5 cmH 2 O or set at an individualized EIT setting. The primary endpoint was the ratio of the arterial oxygen partial pressure to the fractional inspired oxygen (PaO 2 /FiO 2 ). The secondary endpoints included the driving pressure, and dynamic respiratory system compliance (C dyn ). Other outcomes, such as the mean airway pressure (P mean ), mean arterial pressure (MAP), lung complications and the length of hospital stay were explored. Results:The optimal PEEP set by EIT was significantly higher (range from 9-13 cmH 2 O) than the fixed PEEP. PaO 2 /FiO 2 was 47 mmHg higher (95% CI: 7-86 mmHg; P=0.021), C dyn was 4.3 mL/cmH 2 O higher (95% CI: 2.1-6.7 cmH 2 O; P<0.001), and the driving pressure was 3.7 cmH 2 O lower (95% CI: 2.2-5.1 mmH 2 O; P<0.001) at 0.5 h during one-lung ventilation (OLV) in the PEEP EIT group than in the PEEP 5 group. At 1 h during OLV, PaO 2 /FiO 2 was 93 mmHg higher (95% CI: 58-128 mmHg; P<0.001), C dyn was 4.4 mL/cmH 2 O higher (95% CI: 1.9-6.9 mL/cmH 2 O; P=0.001), and the driving pressure was 4.9 cmH 2 O lower (95% CI: 3.8-6.1 cmH 2 O; P<0.001) in the PEEP EIT group than in the PEEP 5 group. PaO 2 /FiO 2 was 107 mmHg higher (95% CI: 56-158 mmHg; P<0.001) in the PEEP EIT group than in the PEEP 5 group during double-lung ventilation at the end of surgery.Conclusions: PEEP values determined with EIT effectively improved oxygenation and lung mechanics during one lung ventilation in elderly patients undergoing thoracoscopic surgery.

Background: Gastroesophageal reflux disease (GERD) was suggested to be associated with exacerbations of chronic obstructive pulmonary disease (COPD) in recent years. The aim of this study was to examine the association between GERD and COPD exacerbation through a meta-analysis. Methods: Databases including EMBASE, MEDLINE, and the Cochrane Central Register of Controlled Trials were searched with a systematic searching strategy for original articles, published until Jan 2019, without language restriction. Results: A total of 13,245 patients from 10 observational articles were included in the meta-analysis. The metaanalysis indicated that GERD is associated with increased risk of COPD exacerbation (OR: 5.37; 95% CI 2.71-10.64). Patients with COPD and GERD had increased number of exacerbation (WMD: 0.48; 95% CI: 0.31 to 0.65). Conclusions: The meta-analysis showed that there was a significant correlation between GERD and COPD exacerbation.

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Background Fungal and bacterial microbiota play an important role in development of asthma. We aim to characterize airway microbiome (mycobiome, bacteriome) and functional genes in asthmatics and controls. Methods Sputum microbiome of controls, untreated asthma patients and inhaled corticosteroid (ICS) receiving patients was detected using high throughput sequencing. Metagenomic sequencing was used to examine the functional genes of microbiome. Results 1. Mycobiome: α diversity was lower in untreated asthma group than that in controls. Mycobiome compositions differed among the three groups. Compared with controls, untreated asthma group has higher abundance of Wallemia, Mortierella and Fusarium. Compared with untreated asthma patients, ICS receiving patients has higher abundance of Fusarium and Mortierella, lower frequency of Wallemia, Alternaria and Aspergillus. 2. Bacteriome: α diversity was lower in untreated asthma group than that in controls. There are some overlaps of bacteriome compositions between controls and untreated asthma patients which were distinct from ICS receiving patients. Untreated asthma group has higher Streptococcus than controls. 3. Potential fungal and bacterial biomarkers of asthma: Trametes, Aspergillus, Streptococcus, Gemella, Neisseria, etc. 4. Correlation network: There are dense and homogenous correlations in controls but a dramatically unbalanced network in untreated asthma and ICS receiving patients, which suggested the existence of disease-specific inter-kingdom and intra-kingdom alterations. 5. Metagenomic analysis: functional pathways were associated with the status of asthma, microbiome and functional genes showed different correlations in different environment. Conclusion We showed mycobiome and bacteriome dysbiosis in asthma featured by alterations in biodiversity, community composition, inter-kingdom and intra-kingdom network. We also observed several functional genes associated with asthma.

This study illustrates that 2′-O-methyl modified gRNAs improve the specificity of the CRISPR–Cas12a system (mg-CRISPR) via suppressing the Cas12a's affinity to off-target DNA and provides an efficient strategy for high-specificity gRNA design.