The shrimp gut is a long digestive structure that includes the Foregut (stomach), Midgut (hepatopancreas) and Hindgut (intestine). Each component has different structural, immunity and digestion roles. Given these three gut digestive tract components’ significance, we examined the bacterial compositions of the Foregut, Hindgut, and Midgut digestive fractions. Those bacterial communities’ structures were evaluated by sequencing the V3 hypervariable region of the 16S rRNA gene, while the functions were predicted by PICRUSt2 bioinformatics workflow. Also, to avoid contamination with environmental bacteria, shrimp were maintained under strictly controlled conditions. The pairwise differential abundance analysis revealed differences among digestive tract fractions. The families Rhodobacteraceae and Rubritalaceae registered higher abundances in the Foregut fraction, while in the Midgut, the families with a higher proportion were Aeromonadaceae, Beijerinckiaceae and Propionibacteriaceae. Finally, the Cellulomonadaceae family resulted in a higher proportion in the Hindgut. Regarding the predicted functions, amino acid and carbohydrate metabolism pathways were the primary functions registered for Foregut microbiota; conversely, pathways associated with the metabolism of lipids, terpenoids and polyketides, were detected in the Midgut fraction. In the Hindgut, pathways like the metabolism of cofactors and vitamins along with energy metabolism were enriched. Structural changes were followed by significant alterations in functional capabilities, suggesting that each fraction’s bacteria communities may carry out specific metabolic functions. Results indicate that white shrimp’s gut microbiota is widely related to the fraction analyzed across the digestive tract. Overall, our results suggest a role for the dominant bacteria in each digestive tract fraction, contributing with a novel insight into the bacterial community.

Background: The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities. Methods: We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses. Results: As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6–V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6–V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.

Research on gut microbiota has primarily focused on bacteria, though eukaryotic microorganisms also play important roles in their host. In fish, the suitability of fecal sampling methods for studying these gut microorganisms remains unclear. This study aimed to evaluate two fecal sampling methods, intestinal scraping and aquarium-bottom sampling, on the diversity and composition of gut microeukaryotes in Nile tilapia (Oreochromis niloticus), highlighting the importance of methodological choices in microeukaryotic studies. Results showed that intestinal scraping provides a more accurate representation of the stable, resident community, avoiding potential bias and emphasizing the critical importance of methodological choices in microeukaryotic research.

The European catfish Silurus glanis L. is a large, adaptable predator whose range continues to expand rapidly in Europe, posing potential environmental, ecological and socio-economic impacts on freshwater ecosystems. Its success results from a combination of species-specific traits and extrinsic abiotic and anthropogenic drivers, which together enhance its ecological adaptability and competitive advantage. While some studies report substantial impacts on fish communities, others find minimal effects, likely due to differences in timing of data collection, lack of baseline data, control sites and assessments of biotic and abiotic interactions. In this review, we: (i) explore the main factors contributing to the invasion success of S. glanis , including both species-specific traits (e.g. trophic plasticity, reproductive strategies, environmental tolerance) and extrinsic drivers, such as propagule pressure, human-assisted dispersal and habitat alterations; (ii) assess its ecological effects across freshwater ecosystems, based on available studies; and (iii) review the methods commonly used for detecting S. glanis , highlighting their pros and cons for species detection. In each section, we highlight key knowledge gaps, such as the lack of experimental studies, limited understanding of long-term impacts on native species and insufficient data on context-dependent effects. These gaps emphasise the urgent need for coordinated research efforts to improve impact assessment and guide effective management strategies.