The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.

Changes in the human gut microbiome are associated with obesity and metabolic syndrome, but the role of the gut virome in both diseases remains largely unknown. We characterized the gut dsDNA virome of 28 school-aged children with healthy normal-weight (NW, n = 10), obesity (O, n = 10), and obesity with metabolic syndrome (OMS, n = 8), using metagenomic sequencing of virus-like particles (VLPs) from fecal samples. The virome classification confirmed the bacteriophages' dominance, mainly composed of Caudovirales. Notably, phage richness and diversity of individuals with O and OMS tended to increase, while the VLP abundance remained the same among all groups. Of the 4,611 phage contigs composing the phageome, 48 contigs were highly prevalent in ≥80% of individuals, suggesting high inter-individual phage diversity. The abundance of several contigs correlated with gut bacterial taxa; and with anthropometric and biochemical parameters altered in O and OMS. To our knowledge, this gut phageome represents one of the largest datasets and suggests disease-specific phage alterations.

Viral metagenomic studies of the human gut microbiota have unraveled the differences in phage populations between health and disease, stimulating interest in phages’ role on bacterial ecosystem regulation. CrAssphage is a common and abundant family in the gut virome across human populations. Therefore, we explored its role in obesity (O) and obesity with metabolic syndrome (OMS) in a children’s cohort. We found a significantly decreased prevalence, diversity, and richness of the crAssphage Alpha subfamily in OMS mainly driven by a decrease in the Alpha_1 and Alpha_4 genera. On the contrary, there was a significant increase in the Beta subfamily in OMS, mainly driven by an increase in Beta_6. Additionally, an overabundance of the Delta_8 genus was observed in OMS. Notably, a decreased abundance of crAssphages was significantly correlated with the overabundance of Bacilli in the same group. The Bacilli class is a robust taxonomical biomarker of O and was also significantly abundant in our OMS cohort. Our results suggest that a loss of stability in the Alpha subfamily of crAssphages is associated with O and OMS. Contrary, an overabundance of the Delta subfamily was found in OMS. Our study advises the importance of considering the dual role (good and evil) of crAssphage subfamilies and their participation in conditions such as O, where we suggest that Alpha loss and Delta gain are associated with obese individuals.

Gut microbiota is associated with the development of metabolic disorders. To study its association with childhood obesity, we performed a cross-sectional study with 46 children (6–12 years old). We collected fecal samples, food-frequency questionnaires (FFQs), and anthropometric measurements. Shotgun metagenomics were used to obtain the microbial taxonomic diversity and metabolic potential. We identified two dietary profiles characterized by complex carbohydrates and proteins (pattern 1) and saturated fat and simple carbohydrates (pattern 2). We classified each participant into normal weight (NW) or overweight and obese (OWOB) using their body mass index (BMI) z-score. The ratio of Firmicutes/Bacteroidetes and alpha diversity were not different between the BMI groups. Genera contributing to beta diversity between NW and OWOB groups included Bacteroides rodentium, B. intestinalis, B. eggerthii, Methanobrevibacter smithii, Eubacterium sp., and Roseburia sp. B. rodentium was associated with lower BMI and dietary pattern 1 intake. Eubacterium sp. and Roseburia sp. were associated with BMI increments and high consumption of dietary pattern 2. Methane and energy metabolism were found enriched in under-represented KEGG pathways of NW group compared to OWOB. Complex dietary and microbiome interaction leads to metabolic differences during childhood, which should be elucidated to prevent metabolic diseases in adolescence and adulthood.

The alteration of gut microbiome composition has been commonly observed in diseases involving inflammation, such as obesity and metabolic impairment. Inflammatory host response in the gut can be a consequence of dietary driven dysbiosis.