'Statistical Irreproducibility' Does Not Improve with Larger Sample Size: How to Quantify and Address Disease Data Multimodality in Human and Animal Research

Antigenic operon fragmentation and diversification mechanism in Bacteroidota impacts gut metagenomics and pathobionts in Crohn's disease microlesions

Comensal Bacteroidota (Bacteroidota) and Enterobacteriacea are often linked to gut inflammation. However, the causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism in Bacteroidota remain unclear. By using the classical lipopolysaccharide/O-antigen 'rfb operon' in Enterobacteriaceae as a surface antigen model (5-rfb-gene-cluster rfbABCDX), and a recent rfbA-typing strategy for strain classification, we characterized the integrity and conservancy of the entire rfb operon in Bacteroidota. Through exploratory analysis of complete genomes and metagenomes, we discovered that most Bacteroidota have the rfb operon fragmented into nonrandom patterns of gene-singlets and doublets/triplets, termed 'rfb-gene-clusters', or rfb-'minioperons' if predicted as transcriptional. To reflect global operon integrity, contiguity, duplication, and fragmentation principles, we propose a six-category (infra/supra-numerary) cataloging system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly Bacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in gut-wall specific micro-niches or micropathologies. Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota have fewer KEGG-pathways despite large genomes. DNA insertions, overrepresenting DNA-exchange-avid (Bacteroides) species, impact our interpretation of functional metagenomics data by inflating by inflating gene-based pathway inference and by overestimating 'extra-species' abundance. Of disease relevance, Bacteroidota species isolated from cavitating/cavernous fistulous tract (CavFT) microlesions in Crohn's Disease have supra-numerary fragmented operons, stimulate TNF-alpha from macrophages with low potency, and do not induce hyperacute peritonitis in mice compared to CavFT Enterobacteriaceae. The impact of 'foreign-DNA' insertions on pro-inflammatory operons, metagenomics, and commensalism/opportunism requires further studies to elucidate their potential for novel diagnostics and therapeutics, and to elucidate the role of co-existing pathobionts in Crohn's disease microlesions.

Sweets and Inflammatory Bowel Disease: Patients Favor Artificial Sweeteners and Diet Foods/Drinks Over Table Sugar and Consume Less Fruits/Vegetables

BACKGROUND

While artificial sweeteners are deemed safe, preclinical studies indicate that artificial sweeteners contribute to gastrointestinal inflammation. Little is known about patients' perceptions and consumption of artificial sweeteners in inflammatory bowel disease (IBD). We surveyed the consumption frequency and beliefs of IBD patients and control participants regarding artificial sweeteners.

METHODS

We surveyed 130 individuals (IBD patients, n = 93; control/non-IBD participants, n = 37) among our tertiary hospital population to determine consumption frequency and beliefs regarding artificial sweeteners (Splenda/sucralose, Stevia/stevia, NutraSweet/Equal/aspartame). A 14-question questionnaire surveyed the frequency of 9 dietary habits, preferences, and beliefs on health benefits of commercial artificial sweeteners, using the following as positive and negative control questions: table sugar, water, fruits/vegetables, and coconut-oil, among others.

RESULTS

Despite the similarity in yes/no consumption data, artificial sweeteners (Q4 t test P = .023) and diet (low calorie) foods/drinks (Q4 t test P = .023) were consumed more frequently by patients with IBD than by control participants, while no difference in preference for water instead of juices/sodas was observed between IBD patients and control participants. Conversely, patients with IBD consumed table sugar less frequently than control participants (Q1 t test-P = .09), in agreement with their reporting of sugary foods as cause of symptoms (P < .01). A positive correlation was observed between artificial sweeteners and fresh fruits/vegetables among the first 31 IBD patients (Spearman P = .017) and confirmed with 62 new IBD patients (r = 0.232; 95% CI, 0.02-0.43; P = .031), indicating that artificial sweeteners are deemed a healthy habit in IBD. Excluding fresh fruits/vegetables, multivariate analyses to develop surrogate principal component analysis indexes of healthy habits confirmed that artificial sweeteners consumption follows healthy preferences among our IBD patients (adjusted P < .0001).

CONCLUSIONS

Consumption of artificial sweeteners correlated with healthy habits, suggesting that our IBD population deemed artificial sweeteners as healthy and/or had preferences for naturally or artificially sweetened flavors and products.

Pork Fat and Meat: A Balance between Consumer Expectations and Nutrient Composition of Four Pig Breeds

Food fat content is one of the most controversial factors from a consumer's point of view. Aim: (1) The trends in consumer attitudes towards pork and the fat and meat compositions in Duroc and Altai meat breeds and Livny and Mangalitsa meat and fat breeds were studied. (2) Methods: Netnographic studies were used to assess Russian consumer purchasing behavior. Protein, moisture, fat, backfat fatty acid content from pigs, longissimus muscles, and backfat from (A) Altai, (L) Livny, and (M) Russian Mangalitsa breeds were compared with those from (D) Russian Duroc. Raman spectroscopy and histology were applied to the backfat analysis. (3) Results: The attitude of Russian consumers to fatty pork is contradictory: consumers note its high fat content as a negative factor, but the presence of fat and intramuscular fat is welcomed because consumers positively associate them with better taste, tenderness, flavor, and juiciness. The fat of the 'lean' D pigs did not show a "healthy" fatty acid ratio, while the n-3 PUFA/n-6 PUFA ratio in the fat of the M pigs was the best, with significant amounts of short-chain fatty acids. The highest UFA content, particularly omega 3 and omega 6 PUFA, was found in the backfat of A pigs with a minimum SFA content. The backfat of L pigs was characterized by a larger size of the adipocytes; the highest monounsaturated and medium chain fatty acid contents and the lowest short-chain fatty acid content; the ratio of omega 3 to omega 6 was 0.07, and the atherogenicity index in L backfat was close to that of D, despite the fact that D pigs are a meat type, while L pigs are a meat and fat type. On the contrary, the thrombogenicity index in L backfat was even lower than the D one. (4) Conclusions: Pork from local breeds can be recommended for functional food production. The requirement to change the promotion strategy for local pork consumption from the position of dietary diversity and health is stated.

The Microbiome Revolution: New Insights for Personalized Medicine

The availability of new culture-independent techniques to study microbes led to the explosion of the gut microbiota revolution in recent decades [...]