Eating less meat is increasingly seen as a healthier, more ethical option. This is leading to growing numbers of flexitarian consumers looking for plant-based meat alternatives (PBMAs) to replace at least some of the animal meat they consume. Popular PBMA products amongst flexitarians, including plant-based mince, burgers, sausages and meatballs, are often perceived as low-quality, ultra-processed foods. However, we argue that the mere industrial processing of ingredients of plant origin does not make a PBMA product ultra-processed by default. To test our hypothesis, we conducted a randomised controlled trial to assess the changes to the gut microbiota of a group of 20 participants who replaced several meat-containing meals per week with meals cooked with PBMA products and compared these changes to those experienced by a size-matched control. Stool samples were subjected to 16S rRNA sequencing. The resulting raw data was analysed in a compositionality-aware manner, using a range of innovative bioinformatic methods. Noteworthy changes included an increase in butyrate metabolising potential—chiefly in the 4-aminobutyrate/succinate and glutarate pathways—and in the joint abundance of butyrate-producing taxa in the intervention group compared to control. We also observed a decrease in the Tenericutes phylum in the intervention group and an increase in the control group. Based on our findings, we concluded that the occasional replacement of animal meat with PBMA products seen in flexitarian dietary patterns can promote positive changes in the gut microbiome of consumers.

Colorectal cancer is the third most commonly diagnosed cancer worldwide. Human gut microbiome plays important roles in protecting against it, as well as contributing to its onset and progression. Identification of specific bacterial taxa associated with early stages of colorectal cancer may help develop effective microbiome-based diagnostics. For precancerous lesions, links of their characteristics to luminal and tumor-associated microbiome composition are to be elucidated. Paired stool and tumor brush biopsy samples were collected from 50 patients with precancerous lesions and early forms of colon cancer; their microbial communities were profiled using high-throughput 16S rRNA sequencing. We showed that the microbiome differences between stool and biopsy samples can be to a high extent computationally corrected. Compositionality-aware statistical analysis of microbiome composition revealed its associations with the number of lesions, lesion type, location and malignization pathway. A major determinant of precancerous lesions malignancy risk—the number of lesions—was positively associated with the abundance of H₂S-producing taxa. Our results contribute to the basis for developing early non-invasive colorectal cancer diagnostics via identifying microorganisms likely participating in early stages of cancer pathogenesis.