Piperacillin/tazobactam for surgical prophylaxis during pancreatoduodenectomy: meta-analysis.

BACKGROUND: Pancreatoduodenectomy is associated with an increased incidence of surgical-site infections, often leading to a significant rise in morbidity and mortality. This trend underlines the inadequacy of traditional antibiotic prophylaxis strategies. Hence, the aim of this meta-analysis was to assess the outcomes of antimicrobial prophylaxis, comparing piperacillin/tazobactam with traditional antibiotics. METHODS: Upon registering in PROSPERO, the international prospective register of systematic reviews (CRD42023479100), a systematic search of various databases was conducted over the interval 2000-2023. This inclusive search encompassed a wide range of study types, including prospective and retrospective cohorts and RCTs. The subsequent data analysis was carried out utilizing RevMan 5.4. RESULTS: A total of eight studies involving 2382 patients who underwent pancreatoduodenectomy and received either piperacillin/tazobactam (1196 patients) or traditional antibiotics (1186 patients) as antibiotic prophylaxis during surgery were included in the meta-analysis. Patients in the piperacillin/tazobactam group had significantly reduced incidences of surgical-site infections (OR 0.43 (95% c.i. 0.30 to 0.62); P < 0.00001) and major surgical complications (Clavien-Dindo grade greater than or equal to III) (OR 0.61 (95% c.i. 0.45 to 0.81); P = 0.0008). Subgroup analysis of surgical-site infections highlighted significantly reduced incidences of superficial surgical-site infections (OR 0.34 (95% c.i. 0.14 to 0.84); P = 0.02) and organ/space surgical-site infections (OR 0.47 (95% c.i. 0.28 to 0.78); P = 0.004) in the piperacillin/tazobactam group. Further, the analysis demonstrated significantly lower incidences of clinically relevant postoperative pancreatic fistulas (grades B and C) (OR 0.67 (95% c.i. 0.53 to 0.83); P = 0.0003) and mortality (OR 0.51 (95% c.i. 0.28 to 0.91); P = 0.02) in the piperacillin/tazobactam group. CONCLUSION: Piperacillin/tazobactam as antimicrobial prophylaxis significantly lowers the risk of postoperative surgical-site infections, major surgical complications (complications classified as Clavien-Dindo grade greater than or equal to III), clinically relevant postoperative pancreatic fistulas (grades B and C), and mortality, hence supporting the implementation of piperacillin/tazobactam for surgical prophylaxis in current practice.

Rationalizing polyp matching criteria in colon capsule endoscopy: an international expert consensus through RAND (modified DELPHI) process.

Background: Colon capsule endoscopy (CCE) has gained momentum as an alternative modality for the investigation of the lower gastrointestinal tract. Of the few challenges that remain, the comparison and - eventually - matching of polyps at different timestamps leads to the potential for double reporting and can contribute to false-positive findings and inaccuracies. With the impending artificial intelligence integration, the risk of double reporting the same polyp due to the lack of information on spatial orientation underscores the necessity for establishing criteria for polyp matching. Objectives: This RAND/University of California, Los Angeles (modified Delphi) process aims to identify the key factors or components used to match polyps within a CCE video. This involves exploring the attributes of each factor to create comprehensive polyp-matching criteria based on international expert consensus. Design: A systematic qualitative study using surveys. Methods: A panel of 11 international CCE experts convened to assess a survey comprised of 60 statements. Participants anonymously rated statement appropriateness on a 1-9 scale (1-3: inappropriate, 4-6: uncertain and 7-9: appropriate). Following a virtual group discussion of the Round 1 results, a Round 2 survey was developed and completed before the final analysis. Results: The factors that were agreed to be essential for polyp matching include (1) timestamp, (2) polyp localization, (3) polyp vascular pattern, (4) polyp size, (5) time interval of the polyp appearance between the green and yellow camera, (6) surrounding tissue, (7) polyp morphology and (8) polyp surface and contour. When five or more factors are satisfied, it was agreed that the comparing polyps are likely the same polyp. Conclusion: This study has established the first complete criteria for polyp matching in CCE. While it might not provide a definitive solution for matching difficult, small and common polyps, these criteria serve as a framework to guide and facilitate the process of polyp-matching.

Creating criteria and standards for matching polyps (abnormal growth in the bowels) on colon capsule video analysis: an international expert agreement using the RAND (modified Delphi process) process Background: Doctors often use colon capsule endoscopy (CCE), a high-tech capsule with two cameras, to record and check for diseases in the small and large bowels as the capsule travels through the intestines. One of the most common conditions in the large bowel is polyps, which are abnormal growths in the lining of the bowel. Comparing and matching polyps in the same video from the capsule can be tricky as they look very similar, leading to the possibility of incorrectly reporting the same polyp twice or more. This can lead to wrong results and inaccuracies. The literature did not have any criteria or standards for matching polyps in CCE before. Aim: Using the RAND/UCLA (modified Delphi) process, this study aims to identify the key factors or components used to match polyps within a CCE video. The goal is to explore each factor and create complete criteria for polyp matching based on the agreement from international experts. Method: A group of 11 international CCE experts came together to evaluate a survey with 60 statements. They anonymously rated each statement on a scale from 1 to 9 (1-3: inappropriate, 4-6: uncertain, and 7-9: appropriate). After discussing the Round 1 results virtually, a Round 2 survey with the same but revised questions was created and completed before the final analysis of their agreement. Results: The main factors for matching polyps are 1) the timing when the polyp was seen, 2) where it is in the bowel, 3) its blood vessel pattern, 4) size, 5) the timing of its appearance between cameras, 6) surrounding tissue features, 7) its shape, and 8) surface features. If five or more of these factors match, the compared polyps are likely the same. Conclusion: This study establishes the first complete criteria for matching polyps in CCE. While it may not provide a definitive solution for matching challenging and small polyps, these criteria serve as a guide to help and make the process of polyp matching easier.

The Diagnostic Utility of Volatile Organic Compounds in Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis.

BACKGROUND: Volatile organic compounds [VOCs] show promise as potential biomarkers of for ulcerative colitis and Crohn's disease, two chronic, idiopathic, gastrointestinal disorders with diagnostic and management challenges. Non-invasive biomarkers aid early diagnosis and management. In this study we review studies of diagnostic accuracy of VOCs in inflammatory bowel disease. METHODS: A systematic search was carried out on the Pubmed and Scopus databases; with 16 studies reviewed and meta-analysis carried out on 10. RESULTS: Meta-analysis of 696 inflammatory bowel disease [IBD] cases against 605 controls revealed a pooled sensitivity and specificity of 87% (95% confidence interval [CI], 0.79 - 0.92) and 83% [95% CI, 0.73 - 0.90], respectively. Area under the curve [AUC] was 0.92. CONCLUSION: VOCs perform very well as non-invasive biomarkers of IBD, with much scope for future improvement and research.

Efficacy and Safety of Ustekinumab for Ulcerative Colitis Through 4 Years: Final Results of the UNIFI Long-Term Maintenance Study.

INTRODUCTION: Ulcerative colitis (UC) is a chronic condition that may require long-term treatment. We report the final efficacy and safety results of the UNIFI long-term extension study of ustekinumab in patients with UC through 4 years. METHODS: Ustekinumab induction responders who completed 44 weeks of maintenance treatment and agreed to enter the long-term extension continued their subcutaneous maintenance therapy (90 mg ustekinumab every 8 or 12 weeks [q8w or q12w] or placebo). Starting at week 56, randomized patients could receive dose adjustment to 90 mg q8w. Symptoms and adverse events were assessed through the study; endoscopic assessment was conducted at week 200. RESULTS: Of the 348 patients randomized to subcutaneous ustekinumab at maintenance baseline (q8w and q12w combined), 55.2% were in symptomatic remission at week 200. A greater proportion of biologic-naive patients (67.2% [117/174]) were in symptomatic remission than those with a history of biologic failure (41.6% [67/161]). Among patients in symptomatic remission at week 200, 96.4% were corticosteroid-free. Of the 171 patients with endoscopic evaluation at week 200, 81.6% (71/87) in the q12w group and 79.8% (67/84) in the q8w group had endoscopic improvement. From weeks 156 to the final safety visit (up to week 220), no deaths, major adverse cardiovascular events, or tuberculosis occurred in patients receiving ustekinumab. Nasopharyngitis, UC worsening, and upper respiratory tract infections were the most frequently reported adverse events. DISCUSSION: The long-term efficacy of ustekinumab maintenance in patients with UC was confirmed through 4 years. No new safety signals were observed. ClinicalTrials.gov number NCT02407236.

Gut microbiota signatures in inflammatory bowel disease.

BACKGROUND: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), affect millions of people worldwide with increasing incidence. OBJECTIVES: Several studies have shown a link between gut microbiota composition and IBD, but results are often limited by small sample sizes. We aimed to re-analyze publicly available fecal microbiota data from IBD patients. METHODS: We extracted original fecal 16S rRNA amplicon sequencing data from 45 cohorts of IBD patients and healthy individuals using the BioProject database at the National Center for Biotechnology Information. Unlike previous meta-analyses, we merged all study cohorts into a single dataset, including sex, age, geography, and disease information, based on which microbiota signatures were analyzed, while accounting for varying technical platforms. RESULTS: Among 2518 individuals in the combined dataset, we discovered a hitherto unseen number of genera associated with IBD. A total of 77 genera associated with CD, of which 38 were novel associations, and a total of 64 genera associated with UC, of which 28 represented novel associations. Signatures were robust across different technical platforms and geographic locations. Reduced alpha diversity in IBD compared to healthy individuals, in CD compared to UC, and altered microbiota composition (beta diversity) in UC and especially in CD as compared to healthy individuals were found. CONCLUSIONS: Combining original microbiota data from 45 cohorts, we identified a hitherto unseen large number of genera associated with IBD. Identification of microbiota features robustly associated with CD and UC may pave the way for the identification of new treatment targets.

Human gut microbiota and endocrinology: paradigm shift from genome to its regulation.

Over the last two decades, it has become clear that the human gut microbiota, a complex community of bacteria, archaea, fungi and viruses, are a critical determinant of human health and disease. Microbiota-derived metabolites provide the host with energy, protect against pathogens, modulate immune and endocrine systems as well as the level of reactive oxygen species in the gut. It has come with no surprise that the human gut microbiota is also linked to the production, utilisation and regulation of host hormones. This implies that the gut microbiota is capable of influencing human behaviour, appetite regulation and metabolism as well as development and immunity. Many of the advances in the field of crosstalk between the gut microbiota and host health, disease and behaviours are generally based on DNA analyses of microbial populations and transplantation of monocultured commensal species to germ-free animals. Recent reports on the activity of the gut microbiota in gastrointestinal diseases such as inflammatory bowel disease and colorectal cancer have highlighted two important points. First, microbial DNA-based abundance does not always correlate with their level of activity and secondly, that metabolism of the complex gut microbiota is regulated by host health status, including the production and metabolism of several human hormones. In this review, we will discuss the lessons learnt from studying the activity and metabolism of the human gut microbiota in health and across gastrointestinal diseases, and how these findings can shape future research on the microbiome-gut-endocrine axis.

Research activity among physicians in the United Kingdom: results from the Royal College of Physicians Census 2022.

We present the results of the 2022 Census of the Federation of Royal Colleges of Physicians of Edinburgh, Glasgow and London on whether physicians undertake research and the barriers they have encountered. 40% of physicians reported that they undertook research alongside their clinical work. Multivariate analysis of the responses showed that men were 1.6 times more likely to say they undertake research than women. The main barriers to undertaking research were having enough time, organisational factors and a lack of confidence. In this opinion piece we discuss some of the challenges and how they could be addressed.

A hybrid machine learning feature selection model-HMLFSM to enhance gene classification applied to multiple colon cancers dataset.

Colon cancer is a significant global health problem, and early detection is critical for improving survival rates. Traditional detection methods, such as colonoscopies, can be invasive and uncomfortable for patients. Machine Learning (ML) algorithms have emerged as a promising approach for non-invasive colon cancer classification using genetic data or patient demographics and medical history. One approach is to use ML to analyse genetic data, or patient demographics and medical history, to predict the likelihood of colon cancer. However, due to the challenges imposed by variable gene expression and the high dimensionality of cancer-related datasets, traditional transductive ML applications have limited accuracy and risk overfitting. In this paper, we propose a new hybrid feature selection model called HMLFSM-Hybrid Machine Learning Feature Selection Model to improve colon cancer gene classification. We developed a multifilter hybrid model including a two-phase feature selection approach, combining Information Gain (IG) and Genetic Algorithms (GA), and minimum Redundancy Maximum Relevance (mRMR) coupling with Particle Swarm Optimization (PSO). We critically tested our model on three colon cancer genetic datasets and found that the new framework outperformed other models with significant accuracy improvements (95%, ~97%, and ~94% accuracies for datasets 1, 2, and 3 respectively). The results show that our approach improves the classification accuracy of colon cancer detection by highlighting important and relevant genes, eliminating irrelevant ones, and revealing the genes that have a direct influence on the classification process. For colon cancer gene analysis, and along with our experiments and literature review, we found that selective input feature extraction prior to feature selection is essential for improving predictive performance.

Clinical utility of colon capsule endoscopy: a moving target?

The purpose of this article is to provide an overview of white light colon capsule endoscopy's current clinical application, concentrating on its most recent developments. Second-generation colon capsule endoscopy (CCE2) is approved by the FDA for use as an adjunctive test in patients with incomplete colonoscopy and within Europe in patients at average risk, those with incomplete colonoscopies or those unwilling to undergo conventional colonoscopies. Since the publication of European Society of GI Endoscopy guidelines on the use of CCE, there has been a significant increase in comparative studies on the diagnostic yield of CCE. This paper discusses CCE2 in further detail. It explains newly developed colon capsule system and the current status on the use of CCE, it also provides a comprehensive summary of systematic reviews on the implementation of CCE in colorectal cancer screening from a methodological perspective. Patients with ulcerative colitis can benefit from CCE2 in terms of assessing mucosal inflammation. As part of this review, performance of CCE2 for assessing disease severity in ulcerative colitis is compared with colonoscopy. Finally, an assessment if CCE can become a cost-effective clinical service overall.

Comparing High- and Low-Model for End-Stage Liver Disease Living-Donor Liver Transplantation to Determine Clinical Efficacy: A Systematic Review and Meta-Analysis (CHALICE Study).

INTRODUCTION: Various studies have demonstrated that low-Model for End-Stage Liver Disease (MELD) living-donor liver transplant (LDLT) recipients have better outcomes with improved patient survival than deceased-donor liver transplantation (DDLT) recipients. LDLT recipients gain the most from being transplanted at MELD <25-30; however, some existing data have outlined that LDLT may provide equivalent outcomes in high-MELD and low-MELD patients, although the term "high" MELD is arbitrarily defined in the literature and various cut-off scores are outlined between 20 and 30, although most commonly, the dividing threshold is 25. The aim of this meta-analysis was to compare LDLT in high-MELD with that in low-MELD recipients to determine patient survival and graft survival, as well as perioperative and postoperative complications. METHODS: Following PROSPERO registration CRD-42021261501, a systematic database search was conducted for the published literature between 1990 and 2021 and yielded a total of 10 studies with 2183 LT recipients; 490 were HM-LDLT recipients and 1693 were LM-LDLT recipients. RESULTS: Both groups had comparable mortality at 1, 3 and 5 years post-transplant (5-year HR 1.19; 95% CI 0.79-1.79; p-value 0.40) and graft survival (HR 1.08; 95% CI 0.72, 1.63; p-value 0.71). No differences were observed in the rates of major morbidity, hepatic artery thrombosis, biliary complications, intra-abdominal bleeding, wound infection and rejection; however, the HM-LDLT group had higher risk for pulmonary infection, abdominal fluid collection and prolonged ICU stay. CONCLUSIONS: The high-MELD LDLT group had similar patient and graft survival and morbidities to the low-MELD LDLT group, despite being at higher risk for pulmonary infection, abdominal fluid collection and prolonged ICU stay. The data, primarily sourced from high-volume Asian centers, underscore the feasibility of living donations for liver allografts in high-MELD patients. Given the rising demand for liver allografts, it is sensible to incorporate these insights into U.S. transplant practices.

Study of capsule endoscopy delivery at scale through enhanced artificial intelligence-enabled analysis (the CESCAIL study).

AIM: Lower gastrointestinal (GI) diagnostics have been facing relentless capacity constraints for many years, even before the COVID-19 era. Restrictions from the COVID pandemic have resulted in a significant backlog in lower GI diagnostics. Given recent developments in deep neural networks (DNNs) and the application of artificial intelligence (AI) in endoscopy, automating capsule video analysis is now within reach. Comparable to the efficiency and accuracy of AI applications in small bowel capsule endoscopy, AI in colon capsule analysis will also improve the efficiency of video reading and address the relentless demand on lower GI services. The aim of the CESCAIL study is to determine the feasibility, accuracy and productivity of AI-enabled analysis tools (AiSPEED) for polyp detection compared with the 'gold standard': a conventional care pathway with clinician analysis. METHOD: This multi-centre, diagnostic accuracy study aims to recruit 674 participants retrospectively and prospectively from centres conducting colon capsule endoscopy (CCE) as part of their standard care pathway. After the study participants have undergone CCE, the colon capsule videos will be uploaded onto two different pathways: AI-enabled video analysis and the gold standard conventional clinician analysis pathway. The reports generated from both pathways will be compared for accuracy (sensitivity and specificity). The reading time can only be compared in the prospective cohort. In addition to validating the AI tool, this study will also provide observational data concerning its use to assess the pathway execution in real-world performance. RESULTS: The study is currently recruiting participants at multiple centres within the United Kingdom and is at the stage of collecting data. CONCLUSION: This standard diagnostic accuracy study carries no additional risk to patients as it does not affect the standard care pathway, and hence patient care remains unaffected.

A Systematic Review and Meta-Analysis: Volatile Organic Compound Analysis in the Detection of Hepatobiliary and Pancreatic Cancers.

BACKGROUND: Hepatobiliary cancers are notoriously difficult to detect, frequently leading to diagnosis in later stages of disease when curative treatment is not an option. The currently used biomarkers such as AFP (alpha-fetoprotein) and CA19.9 lack sensitivity and specificity. Hence, there is an unmet need for an alternative biomarker. AIM: To evaluate the diagnostic accuracy of volatile organic compounds (VOCs) for the detection of hepatobiliary and pancreatic cancers. METHODS: A systematic review of VOCs' use in the detection of hepatobiliary and pancreatic cancers was performed. A meta-analysis was performed using the software R. Heterogeneity was explored through meta-regression analysis. RESULTS: A total of 18 studies looking at 2296 patients were evaluated. Pooled sensitivity and specificity of VOCs for the detection of hepatobiliary and pancreatic cancer were 0.79 (95% CI, 0.72-0.85) and 0.81 (97.5% CI, 0.76-0.85), respectively. The area under the curve was 0.86. Meta-regression analysis showed that the sample media used contributed to heterogeneity. Bile-based VOCs showed the highest precision values, although urine and breath are preferred for their feasibility. CONCLUSIONS: Volatile organic compounds have the potential to be used as an adjunct tool to aid in the early diagnosis of hepatobiliary cancers.

The Fatty Liver, Cirrhosis, and Liver Cancer Study (TENDENCY): Protocol for a Multicenter Case-Control Study.

BACKGROUND: Hepatocellular cancer (HCC) is associated with high mortality, and early diagnosis leads to better survival. Patients with cirrhosis, especially due to nonalcoholic fatty liver disease and viral hepatitis, are at higher risk of developing HCC and form the main screening group. The current screening methods for HCC (6-monthly screening with serum alpha fetoprotein and ultrasound liver) have low sensitivity; hence, there is a need for better screening markers for HCC. OBJECTIVE: Our study, TENDENCY, aims to validate the novel screening markers (methylated septin 9, urinary volatile organic compounds, and urinary peptides) for HCC diagnosis and study these noninvasive biomarkers in liver disease. METHODS: This is a multicenter, nested case-control study, which involves comparing the plasma levels of methylated septin 9 between confirmed HCC cases and patients with cirrhosis (control group). It also includes the comparison of urine samples for the detection of HCC-specific volatile organic compounds and peptides. Based on the findings of a pilot study carried out at University Hospital Coventry & Warwickshire, we estimated our sample size to be 308 (n=88, 29% patients with HCC; n=220, 71% patients with cirrhosis). Urine and plasma samples will be collected from all participants and will be frozen at -80 °C until the end of recruitment. Gas chromatography-mass spectrometry will be used for urinary volatile organic compounds detection, and capillary electrophoresis-mass spectrometry will be used for urinary peptide identification. Real-time polymerase chain reaction will be used for the qualitative detection of plasma methylated septin 9. The study will be monitored by the Research and Development department at University Hospital Coventry & Warwickshire. RESULTS: The recruitment stage was completed in March 2023. The TENDENCY study is currently in the analysis stage, which is expected to finish by November 2023. CONCLUSIONS: There is lack of effective screening tests for hepatocellular cancer despite higher mortality rates. The application of more sensitive plasma and urinary biomarkers for hepatocellular cancer screening in clinical practice will allow us to detect the disease at earlier stages and hence, overall, improve HCC outcomes. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/44264.

Clinicians' Guide to Artificial Intelligence in Colon Capsule Endoscopy-Technology Made Simple.

Artificial intelligence (AI) applications have become widely popular across the healthcare ecosystem. Colon capsule endoscopy (CCE) was adopted in the NHS England pilot project following the recent COVID pandemic's impact. It demonstrated its capability to relieve the national backlog in endoscopy. As a result, AI-assisted colon capsule video analysis has become gastroenterology's most active research area. However, with rapid AI advances, mastering these complex machine learning concepts remains challenging for healthcare professionals. This forms a barrier for clinicians to take on this new technology and embrace the new era of big data. This paper aims to bridge the knowledge gap between the current CCE system and the future, fully integrated AI system. The primary focus is on simplifying the technical terms and concepts in machine learning. This will hopefully address the general "fear of the unknown in AI" by helping healthcare professionals understand the basic principle of machine learning in capsule endoscopy and apply this knowledge in their future interactions and adaptation to AI technology. It also summarises the evidence of AI in CCE and its impact on diagnostic pathways. Finally, it discusses the unintended consequences of using AI, ethical challenges, potential flaws, and bias within clinical settings.

Influence of seasonal and operator variations on diagnostic accuracy of lateral flow devices during the COVID-19 pandemic: a systematic review and meta-analysis.

BACKGROUND: Lateral flow tests (LFT) are point-of-care rapid antigen tests that allow isolation and control of disease outbreaks through convenient, practical testing. However, studies have shown significant variation in their diagnostic accuracy. We conducted a systematic review of the diagnostic accuracy of LFTs for the detection of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) to identify potential factors affecting their performance. METHODS: A systematic search of online databases was carried out to identify studies assessing the sensitivity and specificity of LFTs compared with polymerase chain reaction (PCR) tests. Data were extracted and used to calculate pooled sensitivity and specificity. Meta-regression analysis was conducted to identify covariates influencing diagnostic accuracy. RESULTS: In total, 76 articles with 108,820 test results were identified for analysis. Pooled sensitivity and specificity were 72% (95% confidence interval (CI): 0.68-0.76) and 100% (95% CI: 0.99-1.00), respectively. Staff operation of the LFT showed a statistically significant increase in sensitivity (p=0.04) and specificity (p=0.001) compared with self-operation by the test subjects. The use of LFTs in symptomatic patient subgroups also resulted in higher test sensitivity. CONCLUSION: LFTs display good sensitivity and extremely good specificity for SARS-CoV-2 antigen detection; they become more sensitive in patients with symptoms and when performed by trained professionals.

The Colorectal Cancer Gut Environment Regulates Activity of the Microbiome and Promotes the Multidrug Resistant Phenotype of ESKAPE and Other Pathogens.

Taxonomic composition of the gut microbiota in colorectal cancer (CRC) patients is altered, a newly recognized driving force behind the disease, the activity of which has been overlooked. We conducted a pilot study on active microbial taxonomic composition in the CRC gut via metatranscriptome and 16S rRNA gene (rDNA) sequencing. We revealed sub-populations in CRC (n = 10) and control (n = 10) cohorts of over-active and dormant species, as changes in activity were often independent from abundance. Strikingly, the diseased gut significantly influenced transcription of butyrate producing bacteria, clinically relevant ESKAPE, oral, and Enterobacteriaceae pathogens. A focused analysis of antibiotic (AB) resistance genes showed that both CRC and control microbiota displayed a multidrug resistant phenotype, including ESKAPE species. However, a significant majority of AB resistance determinants of several AB families were upregulated in the CRC gut. We found that environmental gut factors regulated AB resistance gene expression in vitro of aerobic CRC microbiota, specifically acid, osmotic, and oxidative pressures in a predominantly health-dependent manner. This was consistent with metatranscriptome analysis of these cohorts, while osmotic and oxidative pressures induced differentially regulated responses. This work provides novel insights into the organization of active microbes in CRC, and reveals significant regulation of functionally related group activity, and unexpected microbiome-wide upregulation of AB resistance genes in response to environmental changes of the cancerous gut. IMPORTANCE The human gut microbiota in colorectal cancer patients have a distinct population compared to heathy counterparts. However, the activity (gene expression) of this community has not been investigated. Following quantification of both expressed genes and gene abundance, we established that a sub-population of microbes lies dormant in the cancerous gut, while other groups, namely, clinically relevant oral and multi-drug resistant pathogens, significantly increased in activity. Targeted analysis of community-wide antibiotic resistance determinants found that their expression occurs independently of antibiotic treatment, regardless of host health. However, its expression in aerobes, in vitro, can be regulated by specific environmental stresses of the gut, including organic and inorganic acid pressure in a health-dependent manner. This work advances the field of microbiology in the context of disease, showing, for the first time, that colorectal cancer regulates activity of gut microorganisms and that specific gut environmental pressures can modulate their antibiotic resistance determinants expression.

The Colorectal Cancer Microbiota Alter Their Transcriptome To Adapt to the Acidity, Reactive Oxygen Species, and Metabolite Availability of Gut Microenvironments.

The gut microbiome is implicated in the pathology of colorectal cancer (CRC). However, the mechanisms by which the microbiota actively contribute to disease onset and progression remain elusive. In this pilot study, we sequenced fecal metatranscriptomes of 10 non-CRC and 10 CRC patient gut microbiomes and conducted differential gene expression analyses to assess any changed functionality in disease. We report that oxidative stress responses were the dominant activity across cohorts, an overlooked protective housekeeping role of the human gut microbiome. However, expression of hydrogen peroxide and nitric oxide-scavenging genes was diminished and augmented, respectively, positing that these regulated microbial responses have implications for CRC pathology. CRC microbes enhanced expression of genes for host colonization, biofilm formation, genetic exchange, virulence determinants, antibiotic, and acid resistances. Moreover, microbes promoted transcription of genes involved in metabolism of several beneficial metabolites, suggesting their contribution to patient metabolite deficiencies previously solely attributed to tumor cells. We showed in vitro that expression of genes involved in amino acid-dependent acid resistance mechanisms of meta-gut Escherichia coli responded differently to acid, salt, and oxidative pressures under aerobic conditions. These responses were mostly dictated by the host health status of origin of the microbiota, suggesting their exposure to fundamentally different gut conditions. These findings for the first time highlight mechanisms by which the gut microbiota can either protect against or drive colorectal cancer and provide insights into the cancerous gut environment that drives functional characteristics of the microbiome. IMPORTANCE The human gut microbiota has the genetic potential to drive colorectal cancer onset and progression; however, the expression of this genetic potential during the disease has not been investigated. We found that microbial expression of genes that detoxify DNA-damaging reactive oxygen species, which drive colorectal cancer, is compromised in cancer. We observed a greater activation of expression of genes involved in virulence, host colonization, exchange of genetic material, metabolite utilization, defense against antibiotics, and environmental pressures. Culturing gut Escherichia coli of cancerous and noncancerous metamicrobiota revealed different regulatory responses of amino acid-dependent acid resistance mechanisms in a health-dependent manner under environmental acid, oxidative, and osmotic pressures. Here, for the first time, we demonstrate that the activity of microbial genomes is regulated by the health status of the gut in vivo and in vitro and provides new insights for shifts in microbial gene expression in colorectal cancer.