Deviated and early unsustainable stunted development of gut microbiota in children with autism spectrum disorder.

OBJECTIVE: Recent studies have provided insights into the gut microbiota in autism spectrum disorder (ASD); however, these studies were restricted owing to limited sampling at the unitary stage of childhood. Herein, we aimed to reveal developmental characteristics of gut microbiota in a large cohort of subjects with ASD combined with interindividual factors impacting gut microbiota. DESIGN: A large cohort of 773 subjects with ASD (aged 16 months to 19 years), 429 neurotypical (NT) development subjects (aged 11 months to 15 years) were emolyed to determine the dynamics change of gut microbiota across different ages using 16S rRNA sequencing. RESULT: In subjects with ASD, we observed a distinct but progressive deviation in the development of gut microbiota characterised by persistently decreased alpha diversity, early unsustainable immature microbiota, altered aboudance of 20 operational taxonomic units (OTUs), decreased taxon detection rate and 325 deregulated microbial metabolic functions with age-dependent patterns. We further revealed microbial relationships that have changed extensively in ASD before 3 years of age, which were associated with the severity of behaviour, sleep and GI symptoms in the ASD group. This analysis demonstrated that a signature of the combination of 2 OTUs, Veillonella and Enterobacteriaceae, and 17 microbial metabolic functions efficiently discriminated ASD from NT subjects in both the discovery (area under the curve (AUC)=0.86), and validation 1 (AUC=0.78), 2 (AUC=0.82) and 3 (AUC=0.67) sets. CONCLUSION: Our large cohort combined with clinical symptom analysis highlights the key regulator of gut microbiota in the pathogenesis of ASD and emphasises the importance of monitoring and targeting the gut microbiome in future clinical applications of ASD.

RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data.

Drug sensitivity has always been at the core of individualized cancer chemotherapy. However, we have been overwhelmed by large-scale pharmacogenomic data in the era of next-generation sequencing technology, which makes it increasingly challenging for researchers, especially those without bioinformatic experience, to perform data integration, exploration and analysis. To bridge this gap, we developed RNAactDrug, a comprehensive database of RNAs associated with drug sensitivity from multi-omics data, which allows users to explore drug sensitivity and RNA molecule associations directly. It provides association data between drug sensitivity and RNA molecules including mRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) at four molecular levels (expression, copy number variation, mutation and methylation) from integrated analysis of three large-scale pharmacogenomic databases (GDSC, CellMiner and CCLE). RNAactDrug currently stores more than 4 924 200 associations of RNA molecules and drug sensitivity at four molecular levels covering more than 19 770 mRNAs, 11 119 lncRNAs, 438 miRNAs and 4155 drugs. A user-friendly interface enriched with various browsing sections augmented with advance search facility for querying the database is offered for users retrieving. RNAactDrug provides a comprehensive resource for RNA molecules acting in drug sensitivity, and it could be used to prioritize drug sensitivity-related RNA molecules, further promoting the identification of clinically actionable biomarkers in drug sensitivity and drug development more cost-efficiently by making this knowledge accessible to both basic researchers and clinical practitioners. Database URL: http://bio-bigdata.hrbmu.edu.cn/RNAactDrug.

Rain Classroom assisted by WeChat for preliminary online physiology teaching during the COVID-19 pandemic.

Due to the COVID-19 pandemic during spring semester 2020, teachers and students were forced to engage in online instruction. However, there is little evidence on the feasibility of online physiology teaching. This study demonstrated a 3-wk preliminary online physiology course based on Rain Classroom assisted by the mobile application WeChat. Eighty-seven nursing undergraduate students attended an online physiology course during the spring semester of the 2019-2020 academic year from March 9 to March 29. We determined the effects of the online physiology learning based on in-class tests, preclass preparation, and review rates for the course materials. We also measured the students' perceptions and attitudes about online learning with a questionnaire survey. Posttest scores from the first week to the third week in online physiology course (7.22 ± 1.83, 7.68 ± 2.09, and 6.21 ± 2.92, respectively) exceeded the pretest scores (5.32 ± 2.14, 6.26 ± 2.49, and 3.72 ± 2.22, respectively), and this finding was statistically significant (all P < 0.001). Moreover, the pretest scores were significant positive predictors of final grade (all P < 0.01). In addition, the percentage of preclass preparation increased in 3 wk, from 43.68% to 57.47% to 68.97%. From the first week to the third week, the review rate increased from 86.21% to 91.95%; however, the second week was the lowest of all (72.41%). Finally, students' perceptions about their online physiology learning experiences were favorable. In conclusion, online physiology instruction based on Rain Classroom assisted by WeChat was an effective strategy during the COVID-19 pandemic.

Characterizing heterogeneity of non-small cell lung tumour microenvironment to identify signature prognostic genes.

Growing evidence has highlighted the immune response as an important feature of carcinogenesis and therapeutic efficacy in non-small cell lung cancer (NSCLC). This study focused on the characterization of immune infiltration profiling in patients with NSCLC and its correlation with survival outcome. All TCGA samples were divided into three heterogeneous clusters based on immune cell profiles: cluster 1 ('low infiltration' cluster), cluster 2 ('heterogeneous infiltration' cluster) and cluster 3 ('high infiltration' cluster). The immune cells were responsible for a significantly favourable prognosis for the 'high infiltration' community. Cluster 1 had the lowest cytotoxic activity, tumour-infiltrating lymphocytes and interferon-gamma (IFN-γ), as well as immune checkpoint molecules expressions. In addition, MHC-I and immune co-stimulator were also found to have lower cluster 1 expressions, indicating a possible immune escape mechanism. A total of 43 differentially expressed genes (DEGs) that overlapped among the groups were determined based on three clusters. Finally, based on a univariate Cox regression model, prognostic immune-related genes were identified and combined to construct a risk score model able to predict overall survival (OS) rates in the validation datasets.

A frog cathelicidin peptide effectively promotes cutaneous wound healing in mice.

Although cathelicidins in mammals have been well characterized, little is known about the function of cathelicidin in amphibians. In the present study, a novel 24-residue peptide (cathelicidin-NV, ARGKKECKDDRCRLLMKRGSFSYV) belonging to the cathelicidin family was identified from the skin of the plateau frog Nanorana ventripunctata Cathelicidin-NV showed strong wound healing-promoting activity in a murine model with a full-thickness dermal wound. It directly enhanced the proliferation of keratinocyte cells, resulting in accelerated re-epithelialization of the wound site. Cathelicidin-NV also promoted the proliferation of fibroblasts, the differentiation of fibroblasts to myofibroblasts and collagen production in fibroblasts, which are implicated in wound contraction and repair processes. Furthermore, cathelicidin-NV promoted the release of monocyte chemoattractant protein-1, tumor necrosis factor-α, vascular endothelial growth factor and transforming growth factor-ß1 in vivo and in vitro, which are essential in the wound-healing processes such as migration, proliferation and differentiation. The MAPK (ERK, JNK and p38) signaling pathways were involved in the wound healing-promoting effect. Additionally, unlike other cathelicidins, cathelicidin-NV did not have any direct effect on microbes and showed no cytotoxicity and hemolytic activity toward mammalian cells at concentrations up to 200 µg/ml. This current study may facilitate the understanding of the cellular and molecular events that underlie quick wound healing in N. ventripunctata In addition, the combination of these properties makes cathelicidin-NV an excellent candidate for skin wound therapeutics.

Functional Role of SIL1 in Neurodevelopment and Learning.

Background: Sil1 is the causative gene of Marinesco-SjÓ§gren Syndrome (MSS). The mutated Sil1 generates shortened SIL1 protein which will form aggregation and be degraded rapidly. Mental retardation is a major symptom of MSS which suggests a role of SIL1 in the development of the central nervous system, but how SIL1 functions remains unclear. Objectives: The aim of this study is to explore the role of SIL1 in regulating cerebral development and its underlying molecular mechanism. Methods: The basic expression pattern of SIL1 in tissues and cultured cortical neurons is measured by immunostaining and Western blot. The expression of SIL1 is reduced in vitro and in vivo through RNA interference delivered by a lentivirus. The expression of NMDA receptor subunits and the function of the Reelin signaling pathway are then examined by surface biotinylation and Western blot subsequently. Finally, the spatial learning of young mice was assessed by the Barnes maze task. Results: SIL1 deficiency caused a diminished expression of both Reelin receptors and therefore impaired the Reelin signaling pathway. It then inhibited the developmental expression of GluN2A and impaired the spatial learning of 5-week-old mice. Conclusions: These results suggested that SIL1 is required for the development of the central nervous system which is associated with its role in Reelin signaling.

One year study of PM2.5 in Xinxiang city, North China: Seasonal characteristics, climate impact and source.

This study was conducted in order to explore the seasonal characteristics, climate impact and source of PM2.5 in Xinxiang, China. Daily PM2.5 samples were collected at urban site from January to December in 2015. Average PM2.5 concentration was 100.6 ± 65.8 µg m-3 in Xinxiang, which was several times higher than China Ambient Air Quality Standards (GB3095-2012). Secondary inorganic aerosols (SIA) constituted 70% of the total ionic concentrations. The average concentration of SO42- was 6.4 ± 12.0 µg m-3, which ranked the highest among the water-soluble ions analyzed. Seasonal variations of PM2.5 and its major chemical components were significant, most of them with high values in winter and the lowest values in summer, especially with heavier PM2.5 events (more than 200 µg/m3) in December. SIA and OC on polluted days were 2.1-2.3 times higher than those of on clean days. It was estimated that Fe, Li, Na, Mg, Al, K, Ca and Sr were emitted from crustal sources and Pb, Cr, Ni, Cu, Zn, As, Cd and V were emitted from anthropogenic emissions using the EF values. Analysis using the tracer and PCA/MLR revealed that vehicle exhausts were the most important source of PM2.5, which contributed 26.9% of PM2.5 over the whole study period. This study provides detailed composition data and first comprehensive analysis of PM2.5 in Xinxiang during a whole year.

The pollution characteristics of PM2.5 and correlation analysis with meteorological parameters in Xinxiang during the Shanghai Cooperation Organization Prime Ministers' Meeting.

The pollution characteristics of PM2.5 and correlation analysis with meteorological parameters in Xinxiang during the Shanghai Cooperation Organization Prime Ministers' Meeting were investigated. During the whole meeting, nine PM2.5 samples were collected at a suburban site of Xinxiang, and the average concentration of PM2.5 was 122.28 µg m-3. NO3-, NH4+, SO42- accounted for 56.8% of the total water-soluble ions. In addition, with an exception of Cl-, all of water-soluble ions decreased during the meeting. Total concentrations of crustal elements ranged from 6.53 to 185.86 µg m-3, with an average concentration of 52.51 µg m-3, which accounted for 82.5% of total elements. The concentrations of organic carbon and elemental carbon were 7.71 and 1.52 µg m-3, respectively, lower than those before and after the meeting. It is indicated that during the meeting, limiting motor vehicles is to reduce exhaust emissions, delay heating is to reduce the fossil fuel combustion, and other measures are to reduce the concentration of PM2.5. The directly dispersing by mixing layer height increase and the indirectly reducing the formation of secondary aerosol by low relative humidity, and these are the only two key removing mechanisms of PM2.5 in Xinxiang during the meeting.

Mechanisms of fluoroquinolone resistance in Mycobacterium tuberculosis.

Tuberculosis, caused by the pathogen Mycobacterium tuberculosis, is one of the world's deadliest bacterial infectious disease. It is still a global-health threat, particularly because of the drug-resistant forms. Fluoroquinolones, with target of gyrase, are among the drugs used to treat tuberculosis. However, their widespread use has led to bacterial resistance. The molecular mechanisms of fluoroquinolone resistance in mycobacterium tuberculosis have been reported, such as DNA gyrase mutations, drug efflux pumps system, bacterial cell wall thickness and pentapeptide proteins (MfpA) mediated regulation of gyrase. Mutations in gyrase conferring quinolone resistance play important roles and have been extensively studied. Recent studies have shown that the regulation of DNA gyrase affects mycobacterial drug resistance, but the mechanisms, especially by post-translational modification and regulatory proteins, are poorly understood. In this review, we summarize the fluoroquinolone drug development, and the molecular genetics of fluoroquinolone resistance in mycobacteria. Comprehensive understanding of the mechanisms of fluoroquinolone resistance in Mycobacterium tuberculosis will open a new view on understanding drug resistance in mycobacteria and lead to novel strategies to develop new accurate diagnosis methods.

[Spectral reflectance characteristics of dominant plant species at different eco-restoring stages in the semi-arid grassland].

The objective of the research is to apply hyperspectral technique into eco-restoring monitoring. Through the ASD Fields HH portable field spectrometer, the hyperspectral data of dominant plant species in vegetation at different eco-restoring stages in semi-arid grassland in Helin County, Inner Mongolia were collected. The original spectrum reflected data were pretreated by wavelet threshold denoising through ViewSpecPro software before analysis. Using the first derivative spectra between 660 and 800 nm, and the methods of detrended canonical correspondence analysis (DCCA) by Canoco 4. 5 software, the canopy hyperspectral datum of 6 dominant plant species was calculated. The results indicated that the dominant plant species at early succession stage were Setaria viridis and Caragana microphylia, at 5 years eco-restoring stage they were Salsola collina and Caragana microphylia and at late succession stage they were Pinus sylvestnis var. mongolica and Salsola collina, same as field survey. The graph of DCCA indicated that the influential bands of dominant species canopy at early eco-succession stage were short bands, with a large variation among species, the influential bands at 5 years eco-restoring stage were near infrared bands between 1 000 and 1 050 nm, and that at late stage were near infrared bands of 1 040-1 075 nm. The DCCA also showed obviously differences in canopy spectrum among 6 dominant species, and obviously differences among 3 eco-restoring stages.

GluN2B-containing NMDA receptor attenuated neuronal apoptosis in the mouse model of HIBD through inhibiting endoplasmic reticulum stress-activated PERK/eIF2α signaling pathway.

Introduction: Neonatal hypoxic-ischemic brain damage (HIBD) refers to brain damage in newborns caused by hypoxia and reduced or even stopped cerebral blood flow during the perinatal period. Currently, there are no targeted treatments for neonatal ischemic hypoxic brain damage, primarily due to the incomplete understanding of its pathophysiological mechanisms. Especially, the role of NMDA receptors is less studied in HIBD. Therefore, this study explored the molecular mechanism of endogenous protection mediated by GluN2B-NMDAR in HIBD. Method: Hypoxic ischemia was induced in mice aged 9-11 days. The brain damage was examined by Nissl staining and HE staining, while neuronal apoptosis was examined by Hoechst staining and TTC staining. And cognitive deficiency of mice was examined by various behavior tests including Barnes Maze, Three Chamber Social Interaction Test and Elevated Plus Maze. The activation of ER stress signaling pathways were evaluated by Western blot. Results: We found that after HIBD induction, the activation of GluN2B-NMDAR attenuated neuronal apoptosis and brain damage. Meanwhile, the ER stress PERK/eIF2α signaling pathway was activated in a time-dependent manner after HIBE. Furthermore, after selective inhibiting GluN2B-NMDAR in HIBD mice with ifenprodil, the PERK/eIF2α signaling pathway remains continuously activated, leading to neuronal apoptosis, morphological brain damage. and aggravating deficits in spatial memory, cognition, and social abilities in adult mice. Discussion: The results of this study indicate that, unlike its role in adult brain damage, GluN2B in early development plays a neuroprotective role in HIBD by inhibiting excessive activation of the PERK/eIF2α signaling pathway. This study provides theoretical support for the clinical development of targeted drugs or treatment methods for HIBD.

QMD: A new method to quantify microbial absolute abundance differences between groups.

A new method, quantification of microbial absolute abundance differences (QMD), was proposed to estimate the microbial absolute abundance changes of each taxon under different conditions based on the microbial relative abundance. Compared with other methods, QMD displayed greater confidence in understanding microbiome dynamics between groups. We also provide QMD software to investigate common deviations and achieve a better understanding of microbiota changes under different conditions.

DVT: a high-throughput analysis pipeline for locomotion and social behavior in adult Drosophila melanogaster.

BACKGROUND: Drosophila melanogaster is excellent animal model for understanding the molecular basis of human neurological and motor disorders. The experimental conditions and chamber design varied between studies. Moreover, most previously established paradigms focus on fly trace detection algorithm development. A comprehensive understanding on how fly behaves in the chamber is still lacking. RESULTS: In this report, we established 74 unique behavior metrics quantifying spatiotemporal characteristics of adult fly locomotion and social behaviors, of which 49 were newly proposed. By the aiding of the developed analysis pipeline, Drosophila video tracking (DVT), we identified siginificantly different patterns of fly behavior confronted with different chamber height, fly density, illumination and experimental time. Meanwhile, three fly strains which are widely used as control lines, Canton-S(CS), w1118 and Oregon-R (OR), were found to exhibit distinct motion explosiveness and exercise endurance. CONCLUSIONS: We believe the proposed behavior metrics set and pipeline should help identify subtle spatial and temporal differences of drosophila behavior confronted with different environmental factors or gene variants.

Biglycan regulated colorectal cancer progress by modulating enteric neuron-derived IL-10 and abundance of Bacteroides thetaiotaomicron.

Biglycan (BGN) is a proteoglycan with branch chains and highly expressed in enteric neurons in the tumor tissue of colorectal cancer (CRC), which is negatively associated with survival rates in patients with CRC. However, how the proteoglycan promotes the progress of CRC through interacting with bacteria and regulating the immune response of enteric neurons remains largely unknown. In the present study, we found that biglycan deficiency changed tumor distribution in a colitis-associated colon cancer model. Furthermore, we revealed that BGN deficiency inhibits tumor growth in an allograft tumor model and the migration of cancer cell by upregulating interleukin-10 expression in enteric neurons. Significantly, we demonstrated that biglycan deficiency enriched the abundance of Bacteroides thetaiotaomicron through competing with it for chondroitin sulfate to inhibit CRC progress. Our work provided new insights into the interaction between host proteoglycan and gut microbiota as well as the role of enteric neurons in the tumor microenvironment.

Resection of hilar cholangiocarcinoma combined with left hepatectomy and common hepatic arteriectomy without reconstruction.

BACKGROUND/AIMS: To detect the feasibility of using synchronous bile duct, left lobe of liver and common hepatic artery resection without reconstruction to improve the therapeutic efficacy of HC. METHODOLOGY: A total of 19 patients with hilar cholangiocarcinoma undergoing left-sided hepatectomy, hepatic artery resection and right hepatic duct-jejunum anastomosis from June 2005 to May 2010 in our team were included prospectively in this study. RESULTS: One case died from probable sudden myocardial infarction before discharge from hospital. Little bile leakage occurred in one case. No hepatic insufficiency developed in any cases. A follow-up of 6-66 months was applied and 11 cases were still alive at the end. CONCLUSIONS: Hepatic Arteriectomy is viable with lower total bilirubin and the excision weight up to about 30% of the standard liver.

Safety of patients with a graft to body weight ratio less than 0.8% in living donor liver transplantation using right hepatic lobe without middle hepatic vein.

BACKGROUND/AIMS: This study aimed to evaluate the postoperative outcomes of patient with a graft with graft to body weight ratio (GBWR) less than 0.8% after living donor liver transplantation (LDLT) using the right hepatic lobe without middle hepatic vein (MHV). METHODOLOGY: The clinical data of patients who underwent LDLTs using the right hepatic lobe without the MHV, between March 2006 and April 2009, were retrospectively analyzed. Patients were divided into two groups according to the GBWR (group A, GBWR <0.8%; group B, GBWR =0.8%). Preoperative characteristics were statistically analyzed. Postoperative complications were classified by the Clavien classification. The Kaplan-Meier survival analysis with logrank test was used to compare the long-term survival of two groups. RESULTS: The two groups were comparable. Similar incidence of serious postoperative surgical complication (grade =3) was observed between the two groups. The 1-, 3- and 4-year survival rates of the two groups were 81%, 64% and 57%, and 83%, 71% and 64%, respectively. No significant differences were observed. CONCLUSIONS: Small-forsize graft (GBWR <0.8%) can be safely used in adult to- adult LDLT using right hepatic lobe without MHV.

A Frog-Derived Cathelicidin Peptide with Dual Antimicrobial and Immunomodulatory Activities Effectively Ameliorates Staphylococcus aureus-Induced Peritonitis in Mice.

As antimicrobial resistance poses an increasing threat to public health, it is urgent to develop new antimicrobial agents. In this paper, we identify a novel 30-residue peptide (Nv-CATH, NCNFLCKVKQRLRSVSSTSHIGMAIPRPRG) from the skin of the frog Nanorana ventripunctata, which belongs to the cathelicidin family. Nv-CATH exhibited broad-spectrum antimicrobial activity against Gram-positive and Gram-negative bacteria. Nv-CATH significantly protected mice from lethal infections caused by Staphylococcus aureus. Furthermore, the peptide suppressed excessive and harmful inflammatory responses by repressing the production of NO, IL-6, TNF-α, and IL-1ß. The NF-κB-NLRP3 and MAPK inflammatory signaling pathways were involved in the protection in vitro and in vivo. Nv-CATH also modulated macrophage/monocyte and neutrophil trafficking to the infection site by stimulating CXCL1, CXCL2, and CCL2 production in macrophages. Nv-CATH augmented immunocyte-mediated bacterial killing by modestly promoting neutrophils' phagocytosis and PMA-induced NET formation. Thus, Nv-CATH protects mice against bacterial infection by antimicrobial-immunomodulatory duality. The combination of these two characteristics makes Nv-CATH a promising molecule template for the development of novel antimicrobial and antibiotic-resistant agents.

Cathelicidin-NV from Nanorana ventripunctata effectively protects HaCaT cells, ameliorating ultraviolet B-induced skin photoaging.

Cathelicidins are diverse effector molecules in the vertebrate immune system and are related to immune regulation, inflammatory response, wound healing, and blood vessel formation. However, little is known about their free radical scavenging ability, especially in vivo. In this study, a cathelicidin molecule (cathelicidin-NV, ARGKKECKDDRCRLLMKRGSFSYV) previously identified from the spot-bellied plateau frog (Nanorana ventripunctata) (Anura, Dicroglossidae, Dicroglossinae) by us was shown to alleviate ultraviolet B (UVB)-induced skin photoaging in mice. Cathelicidin-NV effectively suppressed cytotoxicity, DNA fragmentation, apoptosis and reduced the protein expression levels of JNK, c-Jun, and MMP-1, which are involved in the regulation of collagen degradation in HaCaT cells induced by UVB irradiation. Furthermore, cathelicidin-NV also scavenged UVB-induced intracellular reactive oxygen species (ROS). Taken together, cathelicidin-NV directly scavenged excessive intracellular ROS to protect HaCaT cells, and subsequently alleviated UVB-induced skin photoaging. This study extends reports on the antioxidant function of the cathelicidin family. In addition, the properties of cathelicidin-NV make it an excellent candidate for the prevention and treatment of UV-induced skin photoaging.

The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging - relevant neural and immune function.

Human longevity has a strong familial and genetic component. Dynamic characteristics of the gut microbiome during aging associated with longevity, neural, and immune function remained unknown. Here, we aim to reveal the synergistic changes in gut microbiome associated with decline in neural and immune system with aging and further obtain insights into the establishment of microbiome homeostasis that can benefit human longevity. Based on 16S rRNA and metagenomics sequencing data for 32 longevity families including three generations, centenarians, elderly, and young groups, we found centenarians showed increased diversity of gut microbiota, severely damaged connection among bacteria, depleted in microbial-associated essential amino acid function, and increased abundance of anti-inflammatory bacteria in comparison to young and elderly groups. Some potential probiotic species, such as Desulfovibrio piger, Gordonibacter pamelaeae, Odoribacter splanchnicus, and Ruminococcaceae bacterium D5 were enriched with aging, which might possibly support health maintenance. The level of Amyloid-ß (Aß) and brain-derived neurotrophic factor (BDNF) related to neural function showed increased and decreased with aging, respectively. The elevated level of inflammatory factors was observed in centenarians compared with young and elderly groups. The enriched Bacteroides fragilis in centenarians might promote longevity through up-regulating anti-inflammatory factor IL-10 expression to mediate the critical balance between health and disease. Impressively, the associated analysis for gut microbiota with the level of Aß, BDNF, and inflammatory factors suggests Bifidobacterium pseudocatenulatum could be a particularly beneficial bacteria in the improvement of impaired neural and immune function. Our results provide a rationale for targeting the gut microbiome in future clinical applications of aging-related diseases and extending life span.Abbreviations: 16S rRNA: 16S ribosomal RNA; MAGs: Metagenome-assembled genomes; ASVs: Amplicon sequence variants; DNA: Deoxyribonucleic acid; FDR: False discovery rate: KEGG: Kyoto Encyclopedia of Genes and Genomes; PCoA: Principal coordinates analysis; PCR: Polymerase chain reaction; PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; Aß: Amyloid-ß (Aß); BDNF: Brain-derived neurotrophic factor.

PM2RA: A Framework for Detecting and Quantifying Relationship Alterations in Microbial Community.

The dysbiosis of gut microbiota is associated with the pathogenesis of human diseases. However, observing shifts in the microbe abundance cannot fully reveal underlying perturbations. Examining the relationship alterations (RAs) in the microbiome between health and disease statuses provides additional hints about the pathogenesis of human diseases, but no methods were designed to detect and quantify the RAs between different conditions directly. Here, we present profile monitoring for microbial relationship alteration (PM2RA), an analysis framework to identify and quantify the microbial RAs. The performance of PM2RA was evaluated with synthetic data, and it showed higher specificity and sensitivity than the co-occurrence-based methods. Analyses of real microbial datasets showed that PM2RA was robust for quantifying microbial RAs across different datasets in several diseases. By applying PM2RA, we identified several novel or previously reported microbes implicated in multiple diseases. PM2RA is now implemented as a web-based application available at http://www.pm2ra-xingyinliulab.cn/.