Microbiome analysis of bile samples in patients with choledocholithiasis and hepatobiliary disorders.

Introduction: The involvement of bacteria in the pathogenesis of biliary tract disease is largely unknown. In this study, we investigated the microbiota of the biliary tissue among adult patients with choledocholithiasis during endoscopic retrograde cholangiography (ERCP). Methods: 16S rDNA sequencing of bile samples, culture, and data of the medication history, underlying diseases, and liver function tests were used for the interpretation of differences in the composition of detected bacterial taxa. Results: The four most common phyla in the bile samples included Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Infection with anaerobic and microaerophilic bacteria showed host specificity, where Fusobacterium, Prevotella, Veillonella, Propionibacterium, Gemella, and Helicobacter coexist in the same patients. Clostridium and Peptoclostridium spp. were detected in 80% and 86% of the patients, where the highest relative abundance rates were detected in patients with elevated alkaline phosphatase (ALP) levels and leukocytosis, respectively. Higher diversity in the bacterial population was detected in patients with common bile duct (CBD) stone, in which the richness of an unclassified member of Alphaproteobacteria plus Helicobacter, Enterobacter/Cronobacter spp., Sphingomonas, Prevotella, Fusobacterium and Aeromonas were detected. Conclusions: Our findings suggested correlations between the presence and relative abundance of several bacterial taxa and CBD stone formation and the effect of medication and underlying diseases on the bile microbial communities. A study on a higher number of bile samples from patients compared with the control group could reveal the role of these bacteria in the pathogenesis of biliary tract disease.

MiR-20b Tissue Expression Level Displays the Diagnostic Value in Papillary Thyroid Carcinoma.

Background: Detection of cancer in patients with thyroid nodules requires sensitive and specific diagnostic modalities that are accurate and inexpensive. This study aimed to identify a potential microRNA(miRNA) panel to detect papillary thyroid carcinoma (PTC). Methods: Following a comprehensive literature review as well as miRNA target predictor databases, Real-time PCR was used to quantify the expression of candidate miRNAs in 59 tissue specimens from 30 patients with PTC and 29 patients with benign nodules. A receiver operating characteristic (ROC) curve analysis was used to assess the accuracy of miRNA expression levels compared to the pathology report as the gold standard. Based on prediction results, four miRNAs, including miR-9, miR-20b, miR-221, and miR-222, were selected to evaluate their expression level in Iranian thyroid samples. Results: A significant difference between the tissue expression level of miR-20b, miR-9, miR-222, and miR-221 was detected in the PTC group compared with non-PTC (P < 0.05). The area under the curves for the included miRs were 1, 0.98, 0.99, 0.98, and 1, respectively. Conclusion: Our results confirmed deregulations of miR-20b as well as miR-222, miR-221, and miR-9 in PTC and, therefore, could be used as a helpful miRNA panel to differentiate PTC from benign nodules, which results in the more efficient clinical management of PTC patients.

Prediction of postnatal abnormal umbilical cord coiling by antenatal evaluation in pregnant women: Diagnostic accuracy study; a systematic review.

STUDY OBJECTIVE: Umbilical cord abnormalities increase neonatal morbidity and mortality. Considering uncertainties about the best time of an antenatal ultrasonography scan to evaluate the umbilical coiling index (UCI), this systematic review was designed to assess the diagnostic accuracy value of antenatal ultrasound assessments to predict abnormal postpartum UCI. METHODS: All observational, cross-sectional, case-control, cohort, and diagnostic accuracy studies up to March 26, 2022, were searched and assessed according to PRISMA guidelines in Ovid, Cochrane, Scopus, PubMed, Web of Science, Embase, Proquest, Science Direct, and Clinical Key databases, and Google Scholar search engine. RESULTS: The total number of 63 190 documents were retrieved from databases. The duplicates (19 272) were removed, 43 918 articles were screened for relevance, and 56 papers were selected for full-text evaluation, resulting in 14 qualified pieces subjected to the quality CASP tools for each type of study. Finally, six articles were evaluated, extracted, and confirmed. Overall, we had 16 evaluations (11 normal pregnancies, 4 gestational diabetes mellitus, and 1 group at risk for small gestational age), from which 9 and 7 were respectively performed in the second and third trimesters. Most of the evaluations considered both hypocoiling and hypercoiling. The sensitivity, specificity, and area under curves (AUCs) change range between the evaluations were 0.09-0.97, 0.59-0.96, and 0.262-0.84, respectively. CONCLUSION: Observing any coiling abnormalities in every trimester, both the second and third, is highly sensitive to predicting abnormal postnatal UCI (pUCI). Conclusively, any detected antenatal abnormality is worth attention. Both trimesters' evaluations are essential, and no superiority is seen for any of them. The systematic review revealed statistical and clinical heterogeneity; a meta-analysis was impossible.

Phylogenetic characterization of rhinovirus and adenovirus in hospitalized children aged ≤ 18 years with severe acute respiratory infection in Iran.

Background and Objectives: Human rhinoviruses (HRVs) and human adenoviruses (HAdVs) are among the most prevalent viruses in hospitalized patients with severe acute respiratory infection (SARI). This study aimed to evaluate the molecular characterization of HRV and HAdV in hospitalized patients with SARI, who aged ≤ 18 years in Tehran, Iran. Materials and Methods: To detect these two viruses, a conventional nested RT-PCR (Reverse transcription-polymerase chain reaction) assay was performed on 264 throat swabs collected from December 2018 to March 2019. The epidemiological data were analyzed and phylogenetic trees were constructed. Results: Of 264 cases with SARI, 36 (13.6%) and 28 (10.6%) were positive for HAdV and HRV respectively. Of 21 HRV sequenced samples, HRV-A (42.9%), HRV-B (9.5%) and HRV-C (47.6%) and of 36 HAdV sequenced samples, HAdV-C6 (38.9%), HAdV-B7 (22.2%), HAdV-B3 (11.1%), HAdV-B16 (5.6%), HAdV-C5 (13.9%), HAdV-C57 (5.6%), HAdV-E4 (2.8%); were detected in children with SARI. Some viral genotypes appeared to cause more severe disease, which may lead to hospitalization. Conclusion: Large-scale studies are recommended to investigate the epidemiology and molecular characterizations through surveillance networks to provide useful information on etiology, seasonality, and demographic associations in patients with SARI.

A systematic review of molecular alterations in invasive non-functioning pituitary adenoma.

PURPOSE: Invasive non-functional pituitary adenomas (NFPAs) constitute 35% of NFPAs. Despite a relatively large body of molecular investigations on the invasiveness of NFPA, the underlying molecular mechanisms of invasiveness are yet to be determined. Herein, we aimed to provide an overview of gene/microRNA(miRNAs) expression alterations in invasive NFPA. METHODS: This article describes a systematic literature review of articles published up to March 23, 2021, on the transcriptional alterations of invasive NFPA. Five digital libraries were searched, and 42 articles in total fulfilled the eligibility criteria. Pathway enrichment was conducted, and protein interactions among the identified deregulated genes were inferred. RESULTS: In total 133 gene/protein transcriptional alterations, comprising 87 increased and 46 decreased expressions, were detected in a collective number of 1001 invasive compared with 1007 non-invasive patients with NFPA. Deregulation of CDH1, PTTG1, CCNB1, SNAI1, SLUG, EZR, and PRKACB, which are associated with epidermal-mesenchymal transition (EMT), was identified. Moreover, six members of the angiogenesis pathway, i.e., VEGFA, FLT1, CCND1, CTNNB1, MYC(c-MYC), and PTTG1, were detected. SLC2A1, FLT1, and VEGFA were also recognized in the hypoxia pathway. Physical interactions of CTNNB1 with FLT1, CCND1, and EZR as well as its indirect interactions with VEGFA, MYC, CCNB1, and PCNA indicate the tight interplay between EMT, angiogenesis, and hypoxia pathways in invasive NFPAs. In addition, Hippo, JAK-STAT, MAPK, Wnt, PI3K-Akt, Ras, TGF-b, VEGF, and ErbB were identified as interwoven signaling pathways. CONCLUSION: In conclusion, invasive NFPA shares very common deregulated signaling pathways with invasive cancers. A large amount of heterogeneity in the reported deregulations in different studies necessitates the validation of the expressional changes of the suggested biomarkers in a large number of patients with invasive NFPA.

Dysregulation of Key Proteinases in Aspergillus fumigatus Induced by Blood Platelets.

BACKGROUND: Aspergillus fumigatus is the most common species causing invasive aspergillosis (IA), a life-threatening infection with more than 80% mortality. Interactions between A. fumigatus and human blood platelets lead to intravascular thrombosis and localized infarcts. To better understand A. fumigatus pathogenesis, we aimed to analyze the genetic basis of interactions between the pathogen and blood platelets. METHODS: A bioinformatic pipeline on microarray gene expression dataset, including analysis of differentially expressed genes (DEGs) using Limma R package and their molecular function, as well as biological pathways identification, was conducted to find the effective genes involved in IA. In the wet phase, the gene expression patterns following fungal exposure to blood platelets at 15, 30, 60, and 180 min were evaluated by quantitative reverse transcriptase-PCR analysis. RESULTS: Three genes encoding aspartic endopeptidases including (Pep1), (Asp f 13), and (ß-glucanase) were the standing candidates. The invasion-promoting fungal proteinase-encoding genes were down-regulated after 30 min of hyphal incubation with blood platelets, and then up-regulated at 60 and 180 min, although only Pep1 was greater than the control at the 60and 180 min time points. Also, the same genes were downregulated in more the clinical isolates relative to the standard strain CBS 144.89. CONCLUSION: Our findings delineate the possible induction of fungal-encoded proteinases by blood platelets. This provides a new research line into A. fumigatus' molecular pathogenesis. Such insight into IA pathogenesis might also guide researchers toward novel platelet-based therapies that involve molecular interventions, especially in IA patients.

Large contribution of copy number alterations in early stage of Papillary Thyroid Carcinoma.

Papillary Thyroid Carcinoma (PTC) accounts for approximately 85% of patients with thyroid cancer. Despite its indolent nature, progression to higher stages is expected in a subgroup of patients. Hence, genomic characterization of the early stages of PTC may help to identify this subgroup, leading to better clinical management. Here, we conducted a comprehensive mutational and somatic copy number alteration (SCNA) investigation on 277 stage one PTC from TCGA. SCNA analysis revealed amplification and deletion of several cancer related genes. We found amplification of 60 oncogenes (Oncs), from which 15 were recurrently observed. Deletion of 58 tumor suppressors (TSs) was also detected. MAPK, PI3K-Akt, Rap1 and Ras were the signaling pathways with large numbers of amplified Oncs. On the other hand, deleted TSs belonged mostly to cell cycle, PI3K-Akt, mTOR and cellular senescence pathways. This suggests that despite heterogeneity in SCNA events, the final results would be the activation/deactivation of a few cancer signaling pathways. Of note, despite large amounts of heterogeneity in stage one PTC, recurrent broad deletion on Chr22 was detected in 21 individuals, leading to deletion of several tumor suppressors. In parallel, the oncogenic/pathogenic mutations in the RTK-RAS and PI3k-Akt pathways were detected. However, no pathogenic mutation was identified in known tumor suppressor genes. In order to identify a potential subgroup of BRAF (V600E) positive patients, who might progress to higher stages, low frequency mutations accompanying BRAF (V600E) were also identified. In conclusion, our findings imply that SCNA have a substantial contribution to early stages of PTC. Experimental validation of the observed genomic alterations could help to stratify patients at the time of diagnosis, and to move toward precision medicine in PTC.

Impact of human rhinoviruses on gene expression in pediatric patients with severe acute respiratory infection.

Human rhinovirus (HRV) is one of the most common viruses, causing mild to severe respiratory tract infections in children and adults. Moreover, it can lead to patients' hospitalization. Nowadays, evaluation of gene expression alterations in host cells due to viral respiratory infections considered essential to understand the viral effects on cells. OBJECTIVE: In this study, we aimed to find important differentially expressed genes (DEGs) related to rhinitis and asthma exacerbation stimulated with Poly (I: C) and then to validate their expression in clinical samples of children how were less than 5 years old, hospitalized with severe acute respiratory infection (SARI) due to HRV infection in comparison with healthy cases. METHODS: Eight candidate genes involved in immunity, viral defense, inflammation, P53 pathway, and viral release processes were selected based on the analysis of a gene expression data set (GSE51392) and gene enrichment analysis. Then quantitative real-time PCR on cDNAs was performed for selected genes. The results were analyzed by Livak method and visualized by GraphPad prism software (8.4.3). RESULT: CXCL10, CMPK2, RSAD2, SERPINA3, TNFAIP6, CXCL14, IVNS1AB, and ZMAT3 were selected based on the enrichment and topological analysis of the constructed protein-protein interaction (PPI) network. Laboratory validation by real-time PCR showed CXCL10, CMPK2, RSAD2, SERPINA3, and TNFAIP6 (belonged to immunity, inflammatory responses and viral defense) were up-regulated, whereas CXCL14 (related to immunity) and IVNS1AB, ZMAT3 (associated to Influenza and P53 pathway) were down-regulated. CONCLUSION: Our results showed, that in children less than 5 years old affected by HRV and hospitalized with SARI, the inflammatory responses, antiviral defense, and type 1 interferon-signaling pathway have significantly affected by viral infection.

Differential miRNAs expression pattern of irradiated breast cancer cell lines is correlated with radiation sensitivity.

Radiotherapy is a fundamental step in the treatment of breast cancer patients. The treatment efficiency is however reduced by the possible onset of radiation resistance. In order to develop the effective treatment approach, it is important to understand molecular basis of radiosensitivity in breast cancer. The purpose of the present study was to investigate different radiation response of breast cancer cell lines, and find out if this response may be related to change in the microRNAs expression profile. MDA-MB-231 and T47D cells were subjected to different doses of radiation, then MTT and clonogenic assays were performed to assess radiation sensitivity. Cytofluorometric and western blot analysis were performed to gain insight into cell cycle distribution and protein expression. MicroRNA sequencing and bioinformatics prediction methods were used to identify the difference in microRNAs expression between two breast cancer cells and the related genes and pathways. T47D cells were more sensitive to radiation respect to MDA-MB-231 cells as demonstrated by a remarkable G2 cell cycle arrest followed by a greater reduction in cell viability and colony forming ability. Accordingly, T47D cells showed higher increase in the phosphorylation of ATM, TP53 and CDK1 (markers of radiation response) and faster and more pronounced increase in RAD51 and γH2AX expression (markers of DNA damage), when compared to MDA-MB-231 cells. The two cell lines had different microRNAs expression profiles with a confirmed significant differential expression of miR-16-5p, which targets cell cycle related genes and predicts longer overall survival of breast cancer patients, as determined by bioinformatics analysis. These results suggest a possible role for miR-16-5p as radiation sensitizing microRNA and as prognostic/predictive biomarker in breast cancer.

Modulation of Toxin-Antitoxin System Rnl AB Type II in Phage-Resistant Gammaproteobacteria Surviving Photodynamic Treatment.

Type II toxin-antitoxin (TA) systems are the particular type of TA modules which take part in different kinds of cellular actions, such as biofilm formation, persistence, stress endurance, defense of the bacterial cell against multiple phage attacks, plasmid maintenance, and programmed cell death in favor of bacterial population. Although several bioinformatics and Pet lab studies have already been conducted to understand the functionality of already discovered TA systems, still, more work in this area is required. Rnl AB type II TA module, which is composed of RnlA toxin and RnlB antitoxin, is a newly discovered type II TA module which takes part in the defense mechanism against T4 bacteriophage attack in Escherichia coli K-12 strain MH1 that has not been widely studied in other bacteria. Because of the significant role of class Gammaproteobacteriacea in a diverse range of health problems, we chose here to focus on this class to survey the presence of the Rnl AB TA module. For better categorization and description of the distribution of this module in this class of bacteria, the corresponding phylogenetic trees are illustrated here. Neighbor-joining and the maximum parsimony methods were used in this study to take a look at the distribution of domains present in RnlA and RnlB proteins, among members of Gammaproteobacteria. Also, the possible roles of photodynamic therapy (PDT) in providing a substrate for better phage therapy are herein discussed.

Block alignment: New representation and comparison method to study evolution of genomes.

Genomes are not random sequences because natural selection has injected information in biological sequences for billions of years. Inspired by this idea, we developed a simple method to compare genomes considering nucleotide counts in subsequences (blocks) instead of their exact sequences. We introduce the Block Alignment method for comparing two genomes and based on this comparison method, define a similarity score and a distance. The presented model ignores nucleotide order in the sequence. On the other hand, in this block comparison method, due to exclusion of point mutations and small size variations, there is no need for high coverage sequencing which is responsible for the high costs of data production and storage; moreover, the sequence comparisons could be performed with higher speed. Phylogenetic trees of two sets of bacterial genomes were constructed and the results were in full agreement with their already constructed phylogenetic trees. Furthermore, a weighted and directed similarity network of each set of bacterial genomes was inferred ab initio by this model. Remarkably, the communities of these networks are in agreement with the clades of the corresponding phylogenetic trees which means these similarity networks also contain phylogenetic information about the genomes. Moreover, the block comparison method was used to distinguish rob(15;21)c-associated iAMP21 and sporadic iAMP21 rearrangements in subgroups of chromosome 21 in acute lymphoblastic leukemia. Our results show a meaningful difference between the number of contigs that mapped to chromosomes 15 and 21 in these cases. Furthermore, the presented block alignment model can select the candidate blocks to perform more accurate analysis and it is capable to find conserved blocks on a set of genomes.

Analysis of Differential Expression of microRNAs and Their Target Genes in Prostate Cancer: A Bioinformatics Study on Microarray Gene Expression Data.

Early diagnosis of prostate cancer (PCa) as the second most common cancer in men is not associated with precise and specific results. Thus, alternate methods with high specificity and sensitivity are needed for accurate and timely detection of PCa. MicroRNAs regulate the molecular pathways involved in cancer by targeting multiple genes. The aberrant expression of the microRNAs has been reported in different cancer types including PCa. In this bioinformatics study, we studied differential expression profiles of microRNAs and their target genes in four PCa gene expression omnibus (GEO) databases. PCa diagnostic biomarker candidates were investigated using bioinformatics tools for analysis of gene expression data, microRNA target prediction, pathway and GO annotation, as well as ROC curves. The results of this study revealed significant changes in the expression of 14 microRNAs and 40 relevant target genes, which ultimately composed four combination panels (miR- 375+96+663/ miR- 133b+143- 3p + 205/ C2ORF72 + ENTPD5 + GLYAT11/LAMB3 + NTNG2+TSLP) as candidate biomarkers capable to distinguish between PCa tumor samples and normal prostate tissue samples. These biomarkers may be suggested for a more accurate early diagnosis of PCa patients along with current diagnostic tests.

Reconstruction of the genome-scale co-expression network for the Hippo signaling pathway in colorectal cancer.

The Hippo signaling pathway (HSP) has been identified as an essential and complex signaling pathway for tumor suppression that coordinates proliferation, differentiation, cell death, cell growth and stemness. In the present study, we conducted a genome-scale co-expression analysis to reconstruct the HSP in colorectal cancer (CRC). Five key modules were detected through network clustering, and a detailed discussion of two modules containing respectively 18 and 13 over and down-regulated members of HSP was provided. Our results suggest new potential regulatory factors in the HSP. The detected modules also suggest novel genes contributing to CRC. Moreover, differential expression analysis confirmed the differential expression pattern of HSP members and new suggested regulatory factors between tumor and normal samples. These findings can further reveal the importance of HSP in CRC.

Comparison of gene co-expression networks in Pseudomonas aeruginosa and Staphylococcus aureus reveals conservation in some aspects of virulence.

Pseudomonas aeruginosa and Staphylococcus aureus are two evolutionary distant bacterial species that are frequently isolated from persistent infections such as chronic infectious wounds and severe lung infections in cystic fibrosis patients. To the best of our knowledge no comprehensive genome scale co-expression study has been already conducted on these two species and in most cases only the expression of very few genes has been the subject of investigation. In this study, in order to investigate the level of expressional conservation between these two species, using heterogeneous gene expression datasets the weighted gene co-expression network analysis (WGCNA) approach was applied to study both single and cross species genome scale co-expression patterns of these two species. Single species co-expression network analysis revealed that in P. aeruginosa, genes involved in quorum sensing (QS), iron uptake, nitrate respiration and type III secretion systems and in S. aureus, genes associated with the regulation of carbon metabolism, fatty acid-phospholipids metabolism and proteolysis represent considerable co-expression across a variety of experimental conditions. Moreover, the comparison of gene co-expression networks between P. aeruginosa and S. aureus was led to the identification of four co-expressed gene modules in both species totally consisting of 318 genes. Several genes related to two component signal transduction systems, small colony variants (SCVs) morphotype and protein complexes were found in the detected modules. We believe that targeting the key players among the identified co-expressed orthologous genes will be a potential intervention strategy to control refractory co-infections caused by these two bacterial species.

Investigation of a common gene expression signature in gastrointestinal cancers using systems biology approaches.

According to GLOBOCAN 2012, the incidence and the mortality rate of colorectal, stomach and liver cancers are the highest among the total gastrointestinal (GI) cancers. Here we aimed to find the common genes and pathways that are simultaneously deregulated in these three malignancies using systems biology approaches. Here we conducted a differential expression analysis on high-quality gene expression datasets of gastric cancer (GC), colorectal cancer (CRC) and hepatocellular carcinoma (HCC). To address the inter gene correlations that were neglected in differential expression studies, we also applied differential co-expression analysis on the understudied datasets. The common significant differentially expressed genes (DEGs) among the three cancers were used for further regulatory and PPI network construction. In parallel the regulatory roles of miRNAs and lncRNAs in the common DEGs were investigated. 23 common DEGs were detected between GC, CRC and HCC. Two cases of potential feed forward loops were identified in the constructed TF-target regulatory network, indicating the probable cross-talk between biological pathways. The result of a vulnerability test on the common PPI network resulted in the finding of three candidates, the simultaneous targeting of which will disintegrate the main parts of the network. The results of the differential co-expression study led to the identification of respectively 7 and 1 common differentially co-expressed pairs of genes between GC and CRC and between CRC and HCC. The results of the differential expression study introduced new common players in CRC, GC and HCC and provided better insights into the molecular characteristics of these GI malignancies. Moreover, we concluded that differential co-expression studies are an essential complement for differential expression studies that just take single differentially expressed genes into account.

Co-expressional conservation in virulence and stress related genes of three Gammaproteobacterial species: Escherichia coli, Salmonella enterica and Pseudomonas aeruginosa.

Gene co-expression analysis is one of the main aspects of systems biology that uses high-throughput gene expression data. In the present study we applied cross-species co-expressional analysis on a module of biofilm and stress response associated genes. We addressed different kinds of stresses in three most intensively studied members of Gammaproteobacteria including Escherichia coli K12, Pseudomonas aeruginosa PAO1 and Salmonella enterica for which large sets of gene expression data are available. Our aim was to evaluate the presence of common stress response strategies adopted by these microorganisms that may be assigned to the other members of Gammaproteobacteria. Results of functional annotation analysis revealed distinct categories among co-expressed genes, most of which concerned biological processes associated with virulence and stress response. Transcriptional regulatory analysis of genes present in co-expressed modules showed that the global stress sigma factor, RpoS, besides several local transcription factors accounts for the observed co-expressional response, and that several cases of feed-forward loops exist between global regulators, local transcription factors and their targets. Our results lend partial support to our underlying assumption of the conservation of core biological processes and regulatory interactions among these related Gammaproteobacteria members. This has led to the implementation of transferring gene function annotations from well-studied Gammaproteobacterial species to less-characterized members. These findings can shed light on the discovery of new drug targets capable of controlling severe infections caused by these groups of bacteria.

Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung.

In polymicrobial communities where several species co-exist in a certain niche and consequently the possibility of interactions among species is very high, gene expression data sources can give better insights in to underlying adaptation mechanisms assumed by bacteria. Furthermore, several possible synergistic or antagonistic interactions among species can be investigated through gene expression comparisons. Lung is one of the habitats harboring several distinct pathogens during severe pulmonary disorders such as chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF). Expression data analysis of these lung residents can help to gain a better understanding on how these species interact with each other within the host cells. The first part of this paper deals with introducing available data sources for the major bacteria responsible for causing lung diseases and their genomic relations. In the second part, the main focus is on the studies concerning gene expression analyses of these species.

Genome-scale co-expression network comparison across Escherichia coli and Salmonella enterica serovar Typhimurium reveals significant conservation at the regulon level of local regulators despite their dissimilar lifestyles.

Availability of genome-wide gene expression datasets provides the opportunity to study gene expression across different organisms under a plethora of experimental conditions. In our previous work, we developed an algorithm called COMODO (COnserved MODules across Organisms) that identifies conserved expression modules between two species. In the present study, we expanded COMODO to detect the co-expression conservation across three organisms by adapting the statistics behind it. We applied COMODO to study expression conservation/divergence between Escherichia coli, Salmonella enterica, and Bacillus subtilis. We observed that some parts of the regulatory interaction networks were conserved between E. coli and S. enterica especially in the regulon of local regulators. However, such conservation was not observed between the regulatory interaction networks of B. subtilis and the two other species. We found co-expression conservation on a number of genes involved in quorum sensing, but almost no conservation for genes involved in pathogenicity across E. coli and S. enterica which could partially explain their different lifestyles. We concluded that despite their different lifestyles, no significant rewiring have occurred at the level of local regulons involved for instance, and notable conservation can be detected in signaling pathways and stress sensing in the phylogenetically close species S. enterica and E. coli. Moreover, conservation of local regulons seems to depend on the evolutionary time of divergence across species disappearing at larger distances as shown by the comparison with B. subtilis. Global regulons follow a different trend and show major rewiring even at the limited evolutionary distance that separates E. coli and S. enterica.