Metabarcoding profiling of microbial diversity associated with trout fish farming

The "Dry-Lab" Side of Food Authentication: Benchmark of Bioinformatic Pipelines for the Analysis of Metabarcoding Data

Next Generation Sequencing Technologies (NGS), particularly metabarcoding, are valuable tools for authenticating foodstuffs and detecting eventual fraudulent practices such as species substitution. This technique, mostly used for the analysis of prokaryotes in several environments (including food), is in fact increasingly applied to identify eukaryotes (e.g., fish, mammals, avian, etc.) in multispecies food products. Besides the "wet-lab" procedures (e.g., DNA extraction, PCR, amplicon purification, etc.), the metabarcoding workflow includes a final "dry-lab" phase in which sequencing data are analyzed using a bioinformatic pipeline (BP). BPs play a crucial role in the accuracy, reliability, and interpretability of the metabarcoding results. Choosing the most suitable BP for the analysis of metabarcoding data could be challenging because it might require greater informatics skills than those needed in standard molecular analysis. To date, studies comparing BPs for metabarcoding data analysis in foodstuff authentication are scarce. In this study, we compared the data obtained from two previous studies in which fish burgers and insect-based products were authenticated using a customizable, ASV-based, and command-line interface BP (BP1) by analyzing the same data with a customizable but OTU-based and graphical user interface BP (BP2). The final sample compositions were compared statistically. No significant difference in sample compositions was highlighted by applying BP1 and BP2. However, BP1 was considered as more user-friendly than BP2 with respect to data analysis streamlining, cost of analysis, and computational time consumption. This study can provide useful information for researchers approaching the bioinformatic analysis of metabarcoding data for the first time. In the field of food authentication, an effective and efficient use of BPs could be especially useful in the context of official controls performed by the Competent Authorities and companies' self-control in order to detect species substitution and counterfeit frauds.

Dietary Protein Quality Affects the Interplay between Gut Microbiota and Host Performance in Nile Tilapia

Dietary protein quality plays a key role in maintaining intestinal mucosal integrity, but also modulates the growth of luminal microorganisms. This work assessed the effect of dietary protein sources on the performance, gut morphology, and microbiome in Nile tilapia. Four isonitrogenous and isolipidic diets comprising equivalent amounts of the protein supply derived from either PLANT, ANIMAL, INSECT, or BACTERIAL (bacterial biomass) sources were fed to triplicate groups of fish (IBW: 12 g) for 46 days. Fish fed the ANIMAL and BACTERIAL diets showed significantly higher weight gains than those fed the PLANT and INSECT diets (p < 0.05). Relative abundance at the phylum level showed that Bacteroidetes, Fusobacteria, and Proteobacteria were the more abundant phyla in tilapia's intestine, while Cetobacterium was the most representative genus in all treatments. Interesting patterns were observed in the correlation between amino acid intake and genus and species abundance. Metabolism prediction analysis showed that BACTERIAL amine and polyamine degradation pathways are modulated depending on diets. In conclusion, different protein sources modulate the relationship between bacteria functional pathways and amino acid intake.

The Bioactive Substances in Spent Black Tea and Arabic Coffee Could Improve the Nutritional Value and Extend the Shelf Life of Sponge Cake after Fortification

The study aimed to evaluate the potential use of spent coffee powder (SCP) and spent tea powder (STP) as bioactive supplements for sponge cake. To achieve this aim, we initially compared the chemical properties of spent tea and coffee powders with those of their raw forms. Subsequently, three supplemented cake blends were prepared (1, 2, and 3% of SCP and STP) to test the effect of their addition on the chemophysical characteristics, sensory attributes, and shelf life of the final products. Our results indicated that spent tea and coffee are prospective materials for polyphenols. Spent tea powder could retain up to 72% (theaflavin trigallate), while spent coffee powder could retain up to 63.9% (1-caffeoylquinic acid) of the identified compounds compared to the raw materials. Furthermore, spent tea and coffee powders contained high levels of dietary fiber (18.95 and 31.65 g/100 g dry weight) and the elements potassium (254.6 and 1218.2 mg/100 g of DW), phosphorus (189.8 and 161.3 mg/100 g of DW), calcium (904.1 and 237.8 mg/100 g of DW), and magnesium (158.8 and 199.6 mg/100 g of DW). In addition, the fortified samples with SCP and STP significantly enhanced the nutritional values while retaining good sensory qualities compared to those of the control sample. Moreover, cakes fortified with the highest concentrations of SCP and STP (3%) showed a significant decrease in malondialdehyde content (MDA; 17.7 and 18.0 μg/g) and microbiological counts (2.4 and 2.5 log cfu/g) compared to the control cake after 14 days of storage. These findings suggest that incorporating SCP and STP into cakes not only enhances their nutritional value but also extends their shelf life. By utilizing these waste products, we can contribute to a more sustainable and ecofriendly food industry.

Comparative Evaluation of Wild and Farmed Rainbow Trout Fish Based on Representative Chemosensory and Microbial Indicators of Their Habitats

Wild and farmed rainbow trout were compared with chemical profiling, chemosensory properties, carbon concentration and isotope analyses, 1- and 2-GC/O-MS, GC-FID, and aroma profile analyses. Results were linked with the prokaryotic and eukaryotic microbiological profile of the fish sources using multivariate statistical analysis. Fish from natural environments proved to have better sensory properties in terms of fruity, sweet, and citrusy attributes, compared to farmed fish. However, the farmed fish were found to have higher nutritional value based on their lipid contents. These differences might relate to the introduction of feed extrudates, which could influence the overall quality of fish products. Thereby, malodor episodes linked to musty/earthy off-odor notes related to odorants including geosmin, β-caryophyllene, (E,Z)-2,4-nonadienal, and (E,E)-2,4-nonadienal. These compounds, in turn, correlated with Asticcacaulis benevestitus, Curvibacter sp., Albidiferax sp., Aquabacterium commune, and Aquabacterium citratiphilum abundance and were further affected by oxygen levels in the water column.

Composition and functionality of bacterioplankton communities in marine coastal zones adjacent to finfish aquaculture

Finfish aquaculture is a fast-growing primary industry and is increasingly common in coastal ecosystems. Bacterioplankton is ubiquitous in marine environment and respond rapidly to environmental changes. Changes in bacterioplankton community are not well understood in semi-enclosed stratified embayments. This study aims to examine aquaculture effects in the composition and functional profiles of the bacterioplankton community using amplicon sequencing along a distance gradient from two finfish leases in a marine embayment. Results revealed natural stratification in bacterioplankton associated to NOx, conductivity, salinity, temperature and PO₄. Among the differentially abundant bacteria in leases, we found members associated with nutrient enrichment and aquaculture activities. Abundant predicted functions near leases were assigned to organic matter degradation, fermentation, and antibiotic resistance. This study provides a first effort to describe changes in the bacterioplankton community composition and function due to finfish aquaculture in a semi-enclosed and highly stratified embayment with a significant freshwater input.

Developing a robust and sensitive analytical method to detect off-flavor compounds in fish

In recirculating aquaculture systems (RAS), off-flavors that accumulate in fish muscle tissue can be problematic in terms of consumer acceptance and the reputation of farmed fish products. Although off-flavors are not toxic at low concentrations, they often give fish muscle earthy, muddy, or other unwanted flavors. Traditionally, muddy off-flavors caused by geosmin (GSM) and 2-methylisoborneol (MIB) have been detected, but a variety of other compounds and flavors have also been identified. In this study, a method based on solid phase micro extraction (SPME) coupled with gas chromatography and mass spectroscopy was developed to identify and quantify 14 off-flavor-inducing compounds in RAS-farmed fish. The selected off-flavors were quantified in circulating water and in fish from a pilot-scale RAS rearing rainbow trout (Oncorhynchus mykiss). The method showed high accuracy and precision with limits of detection and quantification at a low ng L^-1 level. In this study, 13 compounds were found in the fish muscle which decreased in concentrations during the 15-day depuration period. This study showed that off-flavors in fish can also be induced by other compounds besides GSM and MIB. This emphasizes the need for sufficient off-flavor control in the RAS, but also the importance of an accurate and reliable analytical quantitation method.

Molecular Diagnostic Tools Applied for Assessing Microbial Water Quality

Microbial water quality is of vital importance for human, animal, and environmental health. Notably, pathogenically contaminated water can result in serious health problems, such as waterborne outbreaks, which have caused huge economic and social losses. In this context, the prompt detection of microbial contamination becomes essential to enable early warning and timely reaction with proper interventions. Recently, molecular diagnostics have been increasingly employed for the rapid and robust assessment of microbial water quality implicated by various microbial pollutants, e.g., waterborne pathogens and antibiotic-resistance genes (ARGs), imposing the most critical health threats to humans and the environment. Continuous technological advances have led to constant improvements and expansions of molecular methods, such as conventional end-point PCR, DNA microarray, real-time quantitative PCR (qPCR), multiplex qPCR (mqPCR), loop-mediated isothermal amplification (LAMP), digital droplet PCR (ddPCR), and high-throughput next-generation DNA sequencing (HT-NGS). These state-of-the-art molecular approaches largely facilitate the surveillance of microbial water quality in diverse aquatic systems and wastewater. This review provides an up-to-date overview of the advancement of the key molecular tools frequently employed for microbial water quality assessment, with future perspectives on their applications.

Early Neonatal Meconium Does Not Have a Demonstrable Microbiota Determined through Use of Robust Negative Controls with cpn60-Based Microbiome Profiling

Detection of bacterial DNA within meconium is often cited as evidence supporting in utero colonization. However, many studies fail to adequately control for contamination. We aimed to define the microbial content of meconium under properly controlled conditions. DNA was extracted from 141 meconium samples and subjected to cpn60-based microbiome profiling, with controls to assess contamination throughout. Total bacterial loads of neonatal meconium, infant stool, and controls were compared by 16S rRNA quantitative PCR (qPCR). Viable bacteria within meconium were cultured, and isolate clonality was assessed by pulsed-field gel electrophoresis (PFGE). Meconium samples did not differ significantly from controls with respect to read numbers or taxonomic composition. Twenty (14%) outliers with markedly higher read numbers were collected significantly later after birth and appeared more like transitional stool than meconium. Total bacterial loads were significantly higher in stool than in meconium, which did not differ from that of sequencing controls, and correlated well with read numbers. Cultured isolates were most frequently identified as Staphylococcus epidermidis, Enterococcus faecalis, or Escherichia coli, with PFGE indicating high intraspecies diversity. Our findings highlight the importance of robust controls in studies of low microbial biomass samples and argue against meaningful bacterial colonization in utero. Given that meconium microbiome profiles could not be distinguished from sequencing controls, and that viable bacteria within meconium appeared uncommon and largely consistent with postnatal skin colonization, there does not appear to be a meconium microbiota.

IMPORTANCE Much like the recent placental microbiome controversy, studies of neonatal meconium reporting bacterial communities within the fetal and neonatal gut imply that microbial colonization begins prior to birth. However, recent work has shown that placental microbiomes almost exclusively represent contamination from lab reagents and the environment. Here, we demonstrate that prior studies of neonatal meconium are impacted by the same issue, showing that the microbial content of meconium does not differ from negative controls that have never contained any biological material. Our culture findings similarly supported this notion and largely comprised bacteria normally associated with healthy skin. Overall, our work adds to the growing body of evidence against the in utero colonization hypothesis.