Simon J. Keely

Background: Alterations in the gastrointestinal microbiome have been associated with increased anastomotic leak risk. Oral antibiotics and bowel preparations may both reduce anastomotic leaks rates. Objective: Within patients undergoing colorectal surgery, we aimed to examine the impact of oral antibiotic use, bowel preparation and other perioperative factors on the mucosa associated microbiota and investigated association with anastomotic leak rates. Methods: We opportunistically sampled Australian patients undergoing colorectal resection for any indication with anastomosis, mucosal swabs were taken from the proximal and distal extent of the resected specimen immediately after extraction. Methods: A single site, public tertiary referral hospital of 694 beds with an accredited specialist colorectal unit in Newcastle, Australia. Methods: Of 192 patients; 31 patients were identified as receiving oral antibiotics pre-surgery. Thirty-one patients received mechanical preparation and 58 received enema pre-surgery. Methods: The influence of patient factors on mucosa-associated microbiota composition and associations to rate of anastomotic leaks. Results: The leak rate was 15% (N = 28/192). Preoperative oral antibiotic manipulation and bowel preparation minimally affected the mucosa-associated microbiota, but neither were associated with anastomotic leaks. Erythromycin (N = 14/192) had the greatest impact on the mucosa-associated microbiota. Of the different bowel preparation regimes, excluding patients given antibiotics, only fleet enemas (N = 58/161) had a significant impact on the mucosa-associated microbiota. Bowel preparation was not associated with occurrence of anastomotic leaks. There were only subtle differences observed in the mucosa-associated microbiota between anastomotic leaks and non-anastomotic leaks patients. Conclusions: Antibiotic recipient numbers included were modest. Conclusions: This is the largest series of routine colorectal anastomoses for which the mucosa-associated microbiota adjacent the anastomoses was examined. We show that antibiotics and bowel preparation in the preoperative period exert only limited effects on the mucosa-associated microbiota and conclude that there are no obvious mucosa-associated microbiota characteristics that are predictive for an anastomotic leak.

Gastrointestinal conditions such as irritable bowel syndrome (IBS) and inflammatory bowel diseases (IBD) are characterized by alterations in physiological and immune functions. Given the circadian clock influences gastrointestinal physiology and immunity, we hypothesized that the peripheral circadian clock is altered in these patients and might contribute to immune activation associated with IBD and IBS. To investigate this, RNA was extracted from whole blood obtained from control subjects (n = 29), IBD (n = 40 ulcerative colitis, n = 38 Crohn's disease) and IBS (n = 38) participants to investigate peripheral clock gene expression via quantitative PCR. A linear regression model was used to assess the impact of the time of blood collection on clock gene expression. Self-reported data regarding fatigue and sleep indices were compared between patients and control subjects. Gene expression analysis revealed variations in the peripheral circadian system between IBD, IBS and control subjects. The core clock gene CRY1 had higher relative expression in IBS (p = 0.031) and ulcerative colitis patients (p = 0.042) compared with control subjects. Patients with gastrointestinal disease demonstrated poorer quality sleep (IBS p < 0.001, UC p = 0.025 and CD p = 0.007) and more troublesome sleep (IBS p < 0.001, UC p = 0.002 and CD p = 0.009) compared with control subjects. These data suggest a role for CRY1 gene expression in patients experiencing fatigue and highlight a link between circadian dysregulation and the pathophysiology of intestinal disease.

Background: Hypomethylating agents (HMA), such as azacytidine (AZA) and decitabine (DAC), are epigenetic therapies used to treat some patients with acute myeloid leukaemia (AML) and myelodysplastic syndrome. HMAs act in a replication-dependent manner to remove DNA methylation from the genome. However, AML cells targeted by HMA therapy are often quiescent within the bone marrow, where oxygen levels are low. In this study, we investigate the effects of hypoxia on HMA responses in AML cells. Results: AML cell lines (MOLM-13, MV-4-11, HL-60) were treated with DAC (100 nM) or AZA (500-2000 nM) in normoxic (21% O2) and hypoxic (1% O2) conditions. Hypoxia significantly reduced AML cell growth across all cell lines, with no additional effects observed upon HMA treatment. Hypoxia had no impact on the extent of DNA hypomethylation induced by DAC treatment, but limited AZA-induced loss of methylation from the genome. Transcriptional responses to HMA treatment were also altered, with HMAs failing to up-regulate antigen presentation pathways in hypoxia. In particular, cell surface expression of the MHC class II receptor, HLA-DR, was increased by DAC treatment in normoxia, but not hypoxia. Conclusions: Our results suggest that HMA-induced antigen presentation may be impaired by hypoxia. This study highlights the need to consider microenvironmental factors when designing co-treatment strategies to improve HMA therapeutic efficacy.

Dietary gluten triggers symptoms in patients with gluten-related disorders (GRDs) including celiac disease (CeD), non-celiac gluten sensitivity (NCGS), and subsets of patients with functional dyspepsia (FD). The gastrointestinal microbiota is altered in these patients when compared to healthy individuals. As the microbiota is crucial for the hydrolysis of gluten, we hypothesized that the capacity of the microbiota to digest gluten is reduced in these conditions. We systematically reviewed and re-analyzed published datasets to compare gastrointestinal microbiomes of GRD patients and identify signals explaining gluten responses. A systematic search of five databases was conducted to identify studies where the microbiota of CeD, NCGS, or FD patients was analyzed by 16S rRNA amplicon or shotgun metagenomic sequencing and compared to control populations. Where available, raw duodenal microbiota sequence data were re-analyzed with a consistent bioinformatic pipeline. Thirty articles met the inclusion criteria for this systematic review. Microbiota diversity metrics were not impacted by the diseases; however, genera including Streptococcus, Neisseria, and Lactobacillus were commonly altered in GRD patients. Re-analysis of duodenal 16S rRNA data was possible for five included articles but did not identify any consistent differentially abundant taxa. Predicted functional analysis of the microbiome revealed that peptidases including aminopeptidase, proline iminopeptidase, and Xaa-Pro dipeptidase are altered in CeD, NCGS, and FD, respectively. These microbial-derived peptidases hydrolyze bonds in proline-rich gluten peptides. While the gastrointestinal microbiota in patients with GRDs differ from controls, no distinct phenotype links them. However, alterations to the predicted functional capacity of the microbiome to produce gluten-hydrolyzing enzymes suggest that inappropriate digestion of gluten by the microbiome impacts host responses to dietary gluten in these conditions. These findings have implications for therapeutic management of GRDs, as treatment with gluten-degrading enzymes or tailored probiotics could improve disease outcomes by enhancing gluten digestion into non-reactive peptides.

Interactions between diet and gastrointestinal microbiota influence health status and outcomes. Evaluating these relationships requires accurate quantification of dietary variables relevant to microbial metabolism, however current dietary assessment methods focus on dietary components relevant to human digestion only. The aim of this study was to synthesize research on foods and nutrients that influence human gut microbiota and thereby identify knowledge gaps to inform dietary assessment advancements toward better understanding of diet-microbiota interactions. Thirty-eight systematic reviews and 106 primary studies reported on human diet-microbiota associations. Dietary factors altering colonic microbiota included dietary patterns, macronutrients, micronutrients, bioactive compounds, and food additives. Reported diet-microbiota associations were dominated by routinely analyzed nutrients, which are absorbed from the small intestine but analyzed for correlation to stool microbiota. Dietary derived microbiota-relevant nutrients are more challenging to quantify and underrepresented in included studies. This evidence synthesis highlights advancements needed, including opportunities for expansion of food composition databases to include microbiota-relevant data, particularly for human intervention studies. These advances in dietary assessment methodology will facilitate translation of microbiota-specific nutrition therapy to practice.