Bioinformatics and Biology Insights最新文献

{"title":"Pyridine Derivatives as Potential Inhibitors for Coronavirus SARS-CoV-2: A Molecular Docking Study.","authors":"Kamaraj Karthick,&nbsp;Kalaiyar Swarnalatha","doi":"10.1177/11779322221146651","DOIUrl":"https://doi.org/10.1177/11779322221146651","url":null,"abstract":"<p><p>Coronavirus SARS-CoV-2, a causative agent for the global epidemic disease COVID-19, which has a highest modality rate. Several initiatives have been undertaken to repurpose current antiviral medications and tested the classic pyridine derivatives (PyDev), which have showed substantial therapeutic potential against a variety of illnesses and also have several biological functions such as, antibacterial, antiviral, and anti-inflammatory. However, limited reports are available for the treatment of Coronavirus SARS-CoV-2 using PyDev. Hence, the possibilities of the best-described PyDev molecules of powerful Coronavirus SARS-CoV-2 inhibitors have been attempted in this investigation. This study primarily focused on blocking four key targets of Coronavirus SARS-CoV-2 proteins. Terpyridine has shown the greatest inhibitory potential (with a binding energy of -8.8 kcal/mol) against all four coronavirus targets. This study results would pave the potential lead medication for Coronavirus SARS-CoV-2 therapeutic strategies.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/04/d9/10.1177_11779322221146651.PMC10076986.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9289132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Silico Characterization of the Physicochemical and Biological Properties of the Pink (<i>Pleurotus djamor</i> var. <i>salmoneostramineus</i>) Oyster Mushroom Chromoprotein.","authors":"Mónica A Valdez-Solana,&nbsp;Erica K Ventura-García,&nbsp;Iván A Corral-Guerrero,&nbsp;Atahualpa Guzmán de Casa,&nbsp;Claudia Avitia-Domínguez,&nbsp;Alfredo Téllez-Valencia,&nbsp;Erick Sierra-Campos","doi":"10.1177/11779322231154139","DOIUrl":"https://doi.org/10.1177/11779322231154139","url":null,"abstract":"<p><p>Cap color is an important commercial trait for oyster mushrooms. Various pigment constituents determine a diverse color. However, the pigments of oyster mushrooms are still ambiguous. The pink oyster mushroom (<i>Pleurotus salmoneostramineus</i> or <i>Pleurotus djamor</i>) chromoprotein is one of the few proteins belonging to this fungus that has a record of its sequence of amino acid residues. However, even though there are studies about this chromoprotein isolation, purification, and crystallization, the current information focused on its 3-dimensional model and the cofactor and prosthetic group (3H-indol-3-one) binding sites is unreliable and fragmented. Therefore, in this study, using free online servers such as Prot pi, GalaxyWEB, MIB, and CB-Dock2, a structural analysis and the prediction of its physicochemical and biological properties were conducted, to understand the possible function of this chromoprotein. The obtained results showed that this molecule is a protein with a molecular weight of 23 712.5 Da, an isoelectric point of 7.505, with oligomerization capacity in a dimer and glycation in the Ser6 residue. In addition, the participation of the residues Leu5, Leu8, Lys211, Ala214, and Gln215 in the binding of the prosthetic group to the protein was highlighted; as well as Ser6 and Pro7 are important residues for the interaction of the Mg²⁺ ion and eumelanin. Likewise, morphological changes based on different culture conditions (light/dark) showed that this protein is constitutive expressed and independent of blue light. The findings in this study demonstrate that pink chromoprotein is a melanosomal protein, and it possibly has a critical role in melanogenesis and the melanin polymerization. However, more experimental studies are needed to predict a possible mechanism of action and type of enzymatic activity.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0f/ea/10.1177_11779322231154139.PMC9912552.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10707878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MicroRNAs Regulate Tumorigenesis by Downregulating SOCS3 Expression: An <i>In silico</i> Approach.","authors":"Sura Al-Asadi,&nbsp;Hiba Mansour,&nbsp;Ahmed Jwaid Ataimish,&nbsp;Rusul Al-Kahachi,&nbsp;Jamila Rampurawala","doi":"10.1177/11779322231193535","DOIUrl":"https://doi.org/10.1177/11779322231193535","url":null,"abstract":"<p><p>Tumor microenvironment is characterized by the occurrence of significant changes due to disrupted signaling pathways that affect a broad spectrum of cellular activities such as proliferation, differentiation, signaling, invasiveness, migration, and apoptosis. Similarly, a downregulated suppressor of cytokine signaling 3 (SOCS3) promotes increased JAK/STAT function due to aberrant cytokine signaling, which results in increased cell proliferation, differentiation, and migration. Multiple carcinomas including breast cancer, prostate cancer, hepatocellular carcinoma, pancreatic cancer, and colorectal cancer involve the disruption of SOCS3 expression due to microRNA overexpression. MicroRNAs are small, conserved, and non-coding RNA molecules that regulate gene expression through post-transcriptional inhibition and mRNA destabilization. The aim of this study was to identify putative microRNAs that interact with SOCS3 and downregulate its expression. In this study, miRWalk, TargetScan, and miRDB were used to identify microRNAs that interact with SOCS3, whereas RNA22 was utilized to identify the binding sites of 238 significant microRNAs. The tertiary structures of shortlisted microRNAs and SOCS3 regions were predicted through MC Sym and RNAComposer, respectively. For molecular docking, HDOCK was used, which predicted 80 microRNA-messengerRNA complexes and the interactions of the top 5 shortlisted complexes were assessed. The complexes were shortlisted on the basis of least binding affinity score and maximum confidence score. This study identifies the interactions of known (miR-203a-5p) and novel (miR-6756-5p, miR-6732-5p, miR-1203, miR-6887-5p) microRNAs with SOCS3 regions due to their maximum interactions. Identifying the interactions of these microRNAs with SOCS3 will significantly advance the understanding of oncomiRs (miRNAs that are associated with cancer development) in tumor development due to their influence on SOCS3 expression. These insights will assist in future studies to understand the significance of miRNA-SOCS3-associated tumor development and progression.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1d/a0/10.1177_11779322231193535.PMC10493049.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10295523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics Analysis to Uncover the Potential Drug Targets Responsible for <i>Mycobacterium tuberculosis</i> Peptidoglycan and Lysine Biosynthesis.","authors":"Dian Ayu Eka Pitaloka,&nbsp;Afifah Izzati,&nbsp;Siti Rafa Amirah,&nbsp;Luqman Abdan Syakuran,&nbsp;Lalu Muhammad Irham,&nbsp;Athika Darumas Putri,&nbsp;Wirawan Adikusuma","doi":"10.1177/11779322231171774","DOIUrl":"https://doi.org/10.1177/11779322231171774","url":null,"abstract":"<p><p>Drug-resistant tuberculosis (TB), which results mainly from the selection of naturally resistant strains of <i>Mycobacterium tuberculosis</i> (MTB) due to mismanaged treatment, poses a severe challenge to the global control of TB. Therefore, screening novel and unique drug targets against this pathogen is urgently needed. The metabolic pathways of <i>Homo sapiens</i> and MTB were compared using the Kyoto Encyclopedia of Genes and Genomes tool, and further, the proteins that are involved in the metabolic pathways of MTB were subtracted and proceeded to protein-protein interaction network analysis, subcellular localization, drug ability testing, and gene ontology. The study aims to identify enzymes for the unique pathways for further screening to determine the feasibility of the therapeutic targets. The qualitative characteristics of 28 proteins identified as drug target candidates were studied. The results showed that 12 were cytoplasmic, 2 were extracellular, 12 were transmembrane, and 3 were unknown. Furthermore, druggability analysis revealed 14 druggable proteins, of which 12 were novel and responsible for MTB peptidoglycan and lysine biosynthesis. The novel targets obtained in this study are used to develop antimicrobial treatments against pathogenic bacteria. Future studies should further shed light on the clinical implementation to identify antimicrobial therapies against MTB.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d1/13/10.1177_11779322231171774.PMC10176782.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10299669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antibacterial Activity of Economically Important Medicinal Plants in Pakistan Against Different Bacterial Strains.","authors":"Adil Ali,&nbsp;Muhammad Ali,&nbsp;Zonaira Nisar,&nbsp;Syed Muhammad Ali Shah,&nbsp;Imtiaz Mustafa,&nbsp;Jaweria Nisar,&nbsp;Rizwan Asif","doi":"10.1177/11779322231189374","DOIUrl":"https://doi.org/10.1177/11779322231189374","url":null,"abstract":"<p><p>The emergence of medication resistance and unfavorable side effects from existing antibiotics has prompted the quest for novel antimicrobial agents over the last 2 decades. Plant extracts have been shown to have antibacterial effects in numerous studies. The objective of this study was the evaluation of the antibacterial effect of economically important medicinal plants found in Pakistan. <i>Onosma bracteatum</i> (flowers and leaves), <i>Viola odorata</i> (flowers and leaves), <i>Cuscuta reflexa</i> (whole plant), <i>Swertia chirata</i> (whole plant), and <i>Fagonia arabica</i> (whole plant) were used against <i>Bacillus subtilis, Escherichia coli</i>, and <i>Pseudomonas aeruginosa.</i> Water and ethanol extracts were obtained from different parts of the plants. To evaluate the antibacterial effect of these plants, qualitative assay agar well diffusion method was performed. The minimum inhibitory concentration (MIC) was determined by the broth micro dilution method. Results revealed that the highest inhibition zone (18 mm) was shown by ethanol extract of <i>V odorata</i> flower against <i>P aeruginosa</i>. Ethanol extract of <i>C reflexa</i> plants is best for all 3 tested microbes (<i>P aeruginosa, B subtilis</i>, and <i>E coli</i>). The results concluded that all these plants have abilities to fight against these tested bacteria. Ethanol extract of <i>V odorata</i> flower has the highest activity against <i>P aeruginosa</i>.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a7/b3/10.1177_11779322231189374.PMC10392215.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9932957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential Inhibitory Biomolecular Interactions of Natural Compounds With Different Molecular Targets of Diabetes.","authors":"Precious A Akinnusi,&nbsp;Samuel O Olubode,&nbsp;Adebowale A Alade,&nbsp;Aderemi A Ashimi,&nbsp;Olamide L Onawola,&nbsp;Abigail O Agbolade,&nbsp;Adaobi P Emeka,&nbsp;Sidiqat A Shodehinde,&nbsp;Olawole Y Adeniran","doi":"10.1177/11779322231167970","DOIUrl":"https://doi.org/10.1177/11779322231167970","url":null,"abstract":"<p><p>Type II diabetes is an endemic disease and is responsible for approximately 90% to 95% of diabetes cases. The pathophysiological distortions are majorly β-cell dysfunction, insulin resistance, and long-term inflammation, which all progressively unsettle the control of blood glucose levels and trigger microvascular and macrovascular complications. The diverse pathological disruptions which patients with type II diabetes mellitus exhibit precipitate the opinion that different antidiabetic agents, administered in combination, might be required to curb this menace and maintain normal blood glucose. To this end, natural compounds were screened to identify small molecular weight compounds with inhibitory effects on protein tyrosine phosphatase 1B (PTP1B), dipeptidyl-peptidase-4 (DPP-4), and α-amylase. From the result, the top 5 anthocyanins with the highest binding affinity are reported herein. Further ADMET profiling showed moderate pharmacokinetic profiles for these compounds as well as insignificant toxicity. Cyanidin 3-(p-coumaroyl)-diglucoside-5-glucoside (-15.272 kcal/mol), cyanidin 3-O-(6\"-malonyl-3\"-glucosyl-glucoside) (-9.691 kcal/mol), and delphinidin 3,5-O-diglucoside (-12.36 kcal/mol) had the highest binding affinities to PTP1B, DPP-4, and α-amylase, respectively, and can be used in combination to control glucose fluctuations. However, validations must be carried out through further <i>in vitro</i> and <i>in vivo</i> tests.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e2/f6/10.1177_11779322231167970.PMC10134171.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9392846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miR-6087 Might Regulate Cell Cycle-Related mRNAs During Cardiomyogenesis of hESCs.","authors":"Hellen Cristine Machado,&nbsp;Saloe Bispo,&nbsp;Bruno Dallagiovanna","doi":"10.1177/11779322231161918","DOIUrl":"https://doi.org/10.1177/11779322231161918","url":null,"abstract":"MicroRNAs (miRNAs) are small noncoding RNAs that act as negative regulators of gene expression at the post-transcriptional level, promoting mRNA degradation or translation repression. Despite the well-described presence of miRNAs in various human tissues, there is still a lack of information about the relationship between miRNAs and the translation regulation in human embryonic stem cells (hESCs) during cardiomyogenesis. Here, we investigate RNA-seq data from hESCs, focusing on distinct stages of cardiomyogenesis and searching for polysome-bound miRNAs that could be involved in translational regulation. We identify miR-6087 as a differentially expressed miRNA at latest steps of cardiomyocyte differentiation. We analyzed the coexpression pattern between the differentially expressed mRNAs and miR-6087, evaluating whether they are predicted targets of the miRNA. We arranged the genes into an interaction network and identified BLM, RFC4, RFC3, and CCNA2 as key genes of the network. A post hoc analysis of the key genes suggests that miR-6087 could act as a regulator of the cell cycle in hESC during cardiomyogenesis.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c7/ab/10.1177_11779322231161918.PMC10069004.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9612101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selective Non-toxics Inhibitors Targeting DHFR for Tuberculosis and Cancer Therapy: Pharmacophore Generation and Molecular Dynamics Simulation.","authors":"Ghyzlane El Haddoumi,&nbsp;Mariam Mansouri,&nbsp;Houda Bendani,&nbsp;Mohammed Walid Chemao-Elfihri,&nbsp;Jouhaina Kourou,&nbsp;Hanane Abbou,&nbsp;Lahcen Belyamani,&nbsp;Ilham Kandoussi,&nbsp;Azeddine Ibrahimi","doi":"10.1177/11779322231171778","DOIUrl":"https://doi.org/10.1177/11779322231171778","url":null,"abstract":"<p><p>Dihydrofolate reductase (DHFR) is a crucial enzyme that catalyzes the conversion of folic acid. Its reserved properties and significance in both human (h-DHFR) and mycobacterium (mt-DHFR) make it a challenging target for developing drugs against cancer and bacterial infections. Although methotrexate (MTX) is commonly used for cancer therapy and bacterial infections, it has a toxic profile. In this study, we aimed to identify selective and non-toxic inhibitors against h-DHFR and mt-DHFR using an in silico approach. From a data set of 8 412 inhibitors, 11 compounds passed the toxicity and drug-likeness tests, and their interaction with h-DHFR and mt-DHFR was studied by performing molecular docking. To evaluate the inhibitory activity of the compounds against mt-DHFR, five known reference ligands and the natural ligand (dihydrofolate) were used to generate a pharmacophoric map. Two potential selective inhibitors for mt-DHFR and h-DHFR were selected for further investigation using molecular dynamics for 100 ns. As a result, BDBM18226 was identified as the best compound selective for mt-DHFR, non-toxic, with five features listed in the map, with a binding energy of -9.6 kcal/mol. BDBM50145798 was identified as a non-toxic selective compound with a better affinity than MTX for h-DHFR. Molecular dynamics of the two best ligands suggest that they provide more stable, compact, and hydrogen bond interactions with the protein. Our findings could significantly expand the chemical space for new mt-DHFR inhibitors and provide a non-toxic alternative toward h-DHFR for the respective treatment of tuberculosis and cancer therapy.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a9/7d/10.1177_11779322231171778.PMC10170603.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9473443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>S</i>-Adenosyl-l-Homocysteine Exhibits Potential Antiviral Activity Against Dengue Virus Serotype-3 (DENV-3) in Bangladesh: A Viroinformatics-Based Approach.","authors":"Dipok Kumer Shill,&nbsp;Shafina Jahan,&nbsp;Mohammad Mamun Alam,&nbsp;Md Belayet Hasan Limon,&nbsp;Muntasir Alam,&nbsp;Mohammed Ziaur Rahman,&nbsp;Mustafizur Rahman","doi":"10.1177/11779322231158249","DOIUrl":"https://doi.org/10.1177/11779322231158249","url":null,"abstract":"<p><p>Dengue outbreak is one of the concerning issues in Bangladesh due to the annual outbreak with the alarming number of death and infection. However, there is no effective antiviral drug available to treat dengue-infected patients. This study evaluated and screened antiviral drug candidates against dengue virus serotype 3 (DENV-3) through viroinformatics-based analyses. Since 2017, DENV-3 has been the predominant serotype in Bangladesh. We selected 3 non-structural proteins of DENV-3, named NS3, NS4A, and NS5, as antiviral targets. Protein modeling and validation were performed with VERIFY-3D, Ramachandran plotting, MolProbity, and PROCHECK. We found 4 drug-like compounds from DRUGBANK that can interact with these non-structural proteins of DENV-3. Then, the ADMET profile of these compounds was determined by admetSAR2, and molecular docking was performed with AutoDock, SWISSDOCK, PatchDock, and FireDock. Furthermore, they were subjected to molecular dynamics (MD) simulation study using the DESMOND module of MAESTRO academic version 2021-4 (force field OPLS_2005) to determine their solution's stability in a predefined body environment. Two drug-like compounds named Guanosine-5'-Triphosphate (DB04137) and <i>S</i>-adenosyl-l-homocysteine (DB01752) were found to have an effective binding with these 3 proteins (binding energy > 33.47 KJ/mole). We found NS5 protein was stable and equilibrated in a 100 ns simulation run along with a negligible (<3Å) root-mean-square fluctuation value. The root-mean-square deviation value of the <i>S</i>-adenosyl-l-homocysteine-NS5 complex was less than 3Å, indicating stable binding between them. The global binding energy of <i>S</i>-adenosyl-l-homocysteine with NS5 was -40.52 KJ/mole as ∆G. Moreover, these 2 compounds mentioned above are non-carcinogenic according to their ADMET (chemical absorption, distribution, metabolism, excretion, and toxicity) profile (in silico). These outcomes suggest the suitability of <i>S</i>-adenosyl-l-homocysteine as a potential drug candidate for dengue drug discovery research.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/40/40/10.1177_11779322231158249.PMC9974618.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10847932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling.","authors":"Pei-Chen Chen,&nbsp;Ming-Shian Lin,&nbsp;Tien-Ching Lin,&nbsp;Ting-Wei Kang,&nbsp;Jhen-Wei Ruan","doi":"10.1177/11779322231166229","DOIUrl":"https://doi.org/10.1177/11779322231166229","url":null,"abstract":"<p><p>Antibiotic treatment has been shown to cause gut microbiota dysbiosis. However, lacking critical features defining gut microbiota dysbiosis makes it challenging to prevent. By co-occurrence network analysis, we found that despite short antibiotic courses eliminating certain microbial taxa, the <i>Akkermansia</i> genus played the role of a high-centrality hub to maintain microbiota homeostasis. When the antibiotic courses continued, the elimination of <i>Akkermansia</i> induced a significant microbiota remodeling of the gut microbiota networks. Based on this finding, we found that under long-term antibiotic stress, the gut microbiota was rearranged into a stable network with a significantly lower <i>Akkermansiaceae</i>/<i>Lachnospiraceae</i> (A/L) ratio and no microbial hub. By functional prediction analysis, we confirmed that the gut microbiota with a low A/L ratio also had enhanced mobile elements and biofilm-formation functions that may be associated with antibiotic resistance. This study identified A/L ratio as an indicator of antibiotic-induced dysbiosis. This work reveals that besides the abundance of specific probiotics, the hierarchical structure also critically impacts the microbiome function. Co-occurrence analysis may help better monitor the microbiome dynamics than only comparing the differentially abundant bacteria between samples.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":null,"pages":null},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0b/6c/10.1177_11779322231166229.PMC10108413.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9378176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}