The Indigenous Probiotic Lactococcus lactis PH3-05 Enhances the Growth, Digestive Physiology, and Gut Microbiota of the Tropical Gar (Atractosteus tropicus) Larvae.

Probiotics in aquaculture hold promise for enhancing fish health and growth. Due to their increased specificity and affinity for their host, indigenous probiotics may offer isolated and potentially amplified benefits. This study investigated the effects of Lactococcus lactis PH3-05, previously isolated from adults of tropical gar (Atractosteus tropicus), on the growth, survival, digestive enzyme activity, intestinal morphology, expression of barrier and immune genes, and intestinal microbiota composition in the larvae of tropical gar. Larvae were fed with live L. lactis PH3-05 concentrations of 104, 106, and 108 CFU/g for 15 days alongside a control diet without probiotics. Higher concentrations of L. lactis PH3-05 (106 and 108 CFU/g) positively influenced larval growth, increasing hepatocyte area and enterocyte height. The 106 CFU/g dose significantly enhanced survival (46%) and digestive enzyme activity. Notably, the 108 CFU/g dose stimulated increased expression of muc-2 and il-10 genes, suggesting enhanced mucosal barrier function and anti-inflammatory response. Although L. lactis PH3-05 did not significantly change the diversity, structure, or Phylum level composition of intestinal microbiota, which was constituted by Proteobacteria, Bacteroidota, Chloroflexi, and Firmicutes, an increase in Lactobacillus abundance was observed in fish fed with 106 CFU/g, suggesting enhanced probiotic colonization. These results demonstrate that administering L. lactis PH3-05 at 106 CFU/g promotes growth, survival, and digestive health in A. tropicus larvae, establishing it as a promising indigenous probiotic candidate for aquaculture applications.

Deciphering the gut microbiota of zebrafish, the most used fish as a biological model: A meta-analytic approach.

A meta-analytic approach deciphered the taxonomic profile of the zebrafish gut microbiota at different developmental stages. Data (16S rDNA) were systematically searched in databases, selecting those with intestine samples of fish not exposed to a particular treatment or challenge (e.g., pathogens, dietetic tests, xenobiotics, etc.) and obtaining 340 samples to be processed. Results revealed marked differences between the developmental phases. Proteobacteria was the dominant phylum in the larval phase, with a relative abundance of 90%, while the rest of the phyla did not exceed 2%. Vibrio, Aeromonas, Plesiomonas, Pseudomonas, Shewanella, and Acinetobacter were the dominant genera in this phase. Transitional changes were observed after the larvae stage. Proteobacteria still registered high abundance (48%) in the juvenile phase, but Fusobacteria (40%) and Bacteriodota (5.9%) registered considerable increases. Genera, including Cetobacterium, Plesiomonas, Aeromonas, Vibrio, and Flavobacterium, dominated this stage. The phyla Proteobacteria (48%) and Fusobacteria (35%) were strongly established in the adult phase. Cetobacterium was registered as the most abundant genus, followed by Aeromonas, Acinetobacter, Plesiomonas, Vibrio, and ZOR0006 (Firmicutes; 6%). In conclusion, the composition of the intestinal microbiota of zebrafish is consistently determined by two primary phyla, Proteobacteria and Fusobacteria; however, this composition varies depending on the developmental stage. Cetobacterium and Aeromonas are the most relevant genera in juveniles and adults. Finally, these results reveal a consistent pattern of certain bacterial groups in the zebrafish microbiota that could help shape gnotobiotic models (colonized with a specific known bacterial community) or synthetic microbiota (in vitro assembly of microbes), among other approaches.

Gastrointestinal dysbiosis induced by Nocardia sp. infection in tilapia.

Nocardiosis has caused high mortalities among fish cultures; however, the effects of Nocardia infections in the fish gastrointestinal microbiota are unknown. In this research, tilapia was infected with Nocardia sp., to analyze the effect of infection on the gastrointestinal microbiota. Tilapia infected with Nocardia sp. reported a 46 % survival (100 % in non-infected). Moreover, the infection caused severe damage to the stomach microbiota, with a loss of diversity and a significant increase of Proteobacteria (94.8 %), resulting in a negative correlation network between Proteobacteria and other important phyla. Nocardia sp. is an emerging pathogen capable of inducing dysbiosis and causing significant mortalities.

Staphylococcus haemolyticus and Providencia vermicola Infections Occurring in Farmed Tilapia: Two Potentially Emerging Pathogens.

This work aimed to determine the presence of bacterial pathogens in fish with a clinical picture suggestive of infectious disease in Nile tilapia reared in Chiapas, Mexico. Blood and viscera samples were taken from healthy and diseased animals from commercial farms. Clinical and pathological examinations of each individual were performed and samples were collected for bacteriological studies. The bacterial isolates were identified and characterized by culture, biochemical tests, antibiogram, challenge tests and 16S rRNA sequencing. Staphylococcus haemolyticus and Providencia vermicola were isolated from various diseased organisms. The clinical picture caused by Staphylococcus haemolyticus was characterized by appetite disorders, neurological signs, nodulation or ulceration in different areas and congestion or enlargement of internal organs. Providenciosis in juvenile specimens caused a characteristic picture of hemorrhagic septicemia. Challenge tests performed in healthy organisms revealed that both infections caused higher mortality rates in fish (p < 0.05) compared with non-infected specimens, with 100% survival. There was 100% mortality for animals infected with P. vermicola after three days post infection and 45% for those infected with S. haemolyticus. The isolation and identification of two pathogens involved in an infection process were achieved and cataloged as potential causal agents of disease outbreaks in tilapia farming in Mexico. This is the first report of possible bacterial infection caused by S. haemolyticus and P. vermicola in tilapia farms, which are two uncommon but potentially emerging pathogens for the species.

Microbiota plasticity in tilapia gut revealed by meta-analysis evaluating the effect of probiotics, prebiotics, and biofloc.

Tilapia species are among the most cultivated fish worldwide due to their biological advantages but face several challenges, including environmental impact and disease outbreaks. Feed additives, such as probiotics, prebiotics, and other microorganisms, have emerged as strategies to protect against pathogens and promote immune system activation and other host responses, with consequent reductions in antibiotic use. Because these additives also influence tilapia's gut microbiota and positively affect the tilapia culture, we assume it is a flexible annex organ capable of being subject to significant modifications without affecting the biological performance of the host. Therefore, we evaluated the effect of probiotics and other additives ingested by tilapia on its gut microbiota through a meta-analysis of several bioprojects studying the tilapia gut microbiota exposed to feed additives (probiotic, prebiotic, biofloc). A total of 221 tilapia gut microbiota samples from 14 bioprojects were evaluated. Alpha and beta diversity metrics showed no differentiation patterns in relation to the control group, either comparing additives as a group or individually. Results also revealed a control group with a wide dispersion pattern even when these fish did not receive additives. After concatenating the information, the tilapia gut core microbiota was represented by four enriched phyla including Proteobacteria (31%), Fusobacteria (23%), Actinobacteria (19%), and Firmicutes (16%), and seven minor phyla Planctomycetes (1%), Chlamydiae (1%), Chloroflexi (1%), Cyanobacteria (1%), Spirochaetes (1%), Deinococcus Thermus (1%), and Verrucomicrobia (1%). Finally, results suggest that the tilapia gut microbiota is a dynamic microbial community that can plastically respond to feed additives exposure with the potential to influence its taxonomic profile allowing a considerable optimal range of variation, probably guaranteeing its physiological function under different circumstances.

Where are the Penaeids crustins?

Crustins are antimicrobial peptides and members of the four-disulfide core (4-DSC) domain-containing proteins superfamily. To date, crustins have only been reported in crustaceans and possess a structural signature characterized by a single 4-DSC domain and one cysteine-rich region. The high-throughput sequencing technologies have produced vastly valuable genomic information that sometimes dilutes information about previously sequenced molecules. This study aimed (1) to corroborate the loss of valuable descriptive information regarding crustin identification when high throughput sequencing carries out automatic annotation processes and (2) to detect possible crustin sequences reported in Penaeids to attempt a list considering structural similarities, which allows the establishment of phylogenetic relationships based on molecular characteristics. All crustins sequences reported in Penaeids and registered in the databases were obtained. The first list was made with the proteins reported as crustin or carcinin, excluding those that did not meet the structural characteristics. Subsequently, using local alignments, sequences were sought with high similarity even if they had been reported with a different name of crustin but with a probability of being crustin. This broader list, including proteins with high structural similarity, can help establish phylogenetic relationships of shrimp genes and the evolutionary trajectory of this antimicrobial distributed exclusively among crustaceans. Results revealed that in most sequences obtained by Sanger or transcriptomics, which met the structural criteria, the identification was correctly established as crustin. Contrarily, the sequences corresponding to crustins obtained by whole genome sequencing projects were incorrectly classified or not characterized, being momentarily "buried" in the information generated. In addition, the sequences that complied with the criteria of crustin tended to be grouped into species separated by geographical regions; for example, the crustins of the inhabitant shrimp of the American coasts differ from those corresponding to the natives of the Asian coasts. Finally, the results suggest the convenience of annotations considering the previous but correct information, even if such information was generated with previous technologies.

Extraction and characterization of arabinoxylans obtained from nixtamalized brewers' spent grains.

The processes to obtain value-added products from brewers' spent grain, a contaminant industrial waste, require alkaline non-ecofriendly pre-treatments. The arabinoxylans from brewers' spent grain were extracted by nixtamalization evaluating the extraction procedure, antioxidant capacity and molecular characteristics. The best arabinoxylans yields were those extracted with CaO at 100 °C and 25 °C (6.43% and 3.37%, respectively). The antioxidant capacity by 2,2-diphenyl-1-picrylhydrazyl assay of the arabinoxylans after thermal treatment and additional arabinoxylans after thermal treatment proteolysis were 434 and 118 mg TE/g, while by 2,20'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) diammonium salt assay the value was similar (380 µmol TE/g). The intrinsic viscosities and viscosimetric molecular weights were 69 mL/g and 13 kDa for arabinoxylans after thermal treatment, and 15 mL/g and 1.6 kDa for arabinoxylans after thermal treatment proteolysis, respectively. The protein and lignin contents were 3.1% and 6.4% for arabinoxylans after thermal treatment and, 0.9% and 4.6% for arabinoxylans after thermal treatment proteolysis, while their arabinose: xylose ratios were 0.39 and 0.36, with ferulic acid contents of 0.63 and 0.14 mg/g, respectively. Both products of arabinoxylans were molecularly identical by Fourier transform infra-red. Although the purity of the extracted arabinoxylans was improved with proteolysis, their intrinsic viscosity and viscosimetric molecular weight were affected. The extraction of arabinoxylans from brewers' spent grain by CaO nixtamalization alone or after additional proteolysis was successful to obtain purity and good antioxidant capacity.

Detection of human pathogenic bacteria in rectal DNA samples from Zalophus californianus in the Gulf of California, Mexico.

Human intrusions into undisturbed wildlife areas greatly contribute to the emergence of infectious diseases. To minimize the impacts of novel emerging infectious diseases (EIDs) on human health, a comprehensive understanding of the microbial species that reside within wildlife species is required. The Gulf of California (GoC) is an example of an undisturbed ecosystem. However, in recent decades, anthropogenic activities within the GoC have increased. Zalophus californianus has been proposed as the main sentinel species in the GoC; hence, an assessment of sea lion bacterial microbiota may reveal hidden risks for human health. We evaluated the presence of potential human pathogenic bacterial species from the gastrointestinal (GI) tracts of wild sea lions through a metabarcoding approach. To comprehensively evaluate this bacterial consortium, we considered the genetic information of six hypervariable regions of 16S rRNA. Potential human pathogenic bacteria were identified down to the species level by integrating the RDP and Pplacer classifier outputs. The combined genetic information from all analyzed regions suggests the presence of at least 44 human pathogenic bacterial species, including Shigella dysenteriae and Bacillus anthracis. Therefore, the risks of EIDs from this area should be not underestimated.

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei.

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.

Granulomatous bacterial diseases in fish: An overview of the host's immune response.

Bacterial diseases represent the main impediment to the development of fish aquaculture. Granulomatous diseases caused by bacteria lead to fish culture losses by high mortality rates and slow growth. Bacteria belonging to genera Streptococcus spp., Mycobacterium sp., Nocardia sp., Francisella sp., and Staphylococcus sp. have been implicated in the development of granulomatous processes. The granuloma formation and the fish's immune response continue to be the subject of scientific research. In fish, the first defense line is constituted by non-specific humoral factors through growth-inhibiting substances such as transferrin and antiproteases, or lytic effectors as lysozyme and antimicrobial peptides, and linking with non-specific phagocyte responses. If the first line is breached, fish produce antibody constituents for a specific humoral defense inhibiting bacterial adherence, as well as the mobilization of non-phagocytic host cells and counteracting toxins from bacteria. However, bacteria causing granulomatous diseases can be persistent microorganisms, difficult to eliminate that can cause chronic diseases, even using some immune system components to survive. Understanding the infectious process leading to granulomatosis and how the host's immune system responds against granulomatous diseases is crucial to know more about fish immunology and develop strategies to overcome granulomatous diseases.

Exploring the garlic (Allium sativum) properties for fish aquaculture.

The aquaculture industry's rapid growth to meet commercial demand can trigger an outbreak of infectious diseases due to high-density farming. Antibiotic overuse and misuse in fish farming and its global health consequences have led to searching for more natural alternatives such as medicinal plants. In this sense, garlic (Allium sativum) has different bioactive compounds with biological properties for animal health. Among them are the ajoene, alliin, and allicin, which confer biological properties such as growth promotion, antimicrobial, antiviral, antioxidant, and antiparasitic. Ways to use garlic in aquaculture include oil, fresh mash, aqueous extract, and garlic powder. The powder presentation is the most used in aquaculture; it is generally applied by oral administration, adding to the feed, and the dose used ranges from 0.05 to 40 g/kg of feed. Garlic has been used in the aquaculture of different species such as rainbow trout (Oncorhynchus mykiss), spotted grouper (Epinephelus coioides), catfish (Clarias gariepinus), tilapia (Oreochromis niloticus), guppy fish (Poecilia reticulata), goldfish (Carassius auratus), and barramundi (Lates calcarifer). In addition to its properties, garlic's usage became popular, thanks to its low cost, easy incorporation into food, and little environmental impact. Therefore, its application can be an effective solution to combat diseases, improve organisms' health using natural supplies, and as an alternative to antibiotics. This review reports and discusses plant-derived products' beneficial properties, emphasizing garlic and its usages in fish aquaculture.

Highly cross-linked arabinoxylans microspheres as a microbiota-activated carrier for colon-specific insulin delivery.

In vivo evaluation of arabinoxylans (AX) microspheres showed to protect insulin from degradation in the upper gastrointestinal tract and carrier insulin to colon. Insulin-loaded AX microspheres (50 UI/kg) decreased blood glucose level by 39% in diabetic rats with a maximum effect at 18 h post-administration, indicating that insulin remains bioactive. The continuous administration (4 days) of insulin-loaded AX microspheres improved the polyuria and increased the production of short-chain fatty acids, as well as Bifidobacterium and Bacteroides in diabetic rats compared to untreated diabetic rats. AX microspheres are a potential microbiota-activated carrier for colon-specific drug delivery and could be useful as a complementary treatment for diabetes.

Exploring the Milk-Clotting and Proteolytic Activities in Different Tissues of Vallesia glabra: a New Source of Plant Proteolytic Enzymes.

Proteolytic enzymes are widely distributed in nature, playing essential roles in important biological functions. Recently, the use of plant proteases at the industrial level has mainly increased in the food industry (e.g., cheesemaking, meat tenderizing, and protein hydrolysate production). Current technological and scientific advances in the detection and characterization of proteolytic enzymes have encouraged the search for new natural sources. Thus, this work aimed to explore the milk-clotting and proteolytic properties of different tissues of Vallesia glabra. Aqueous extracts from the leaves, fruits, and seeds of V. glabra presented different protein profiles, proteolytic activity, and milk-clotting activity. The milk-clotting activity increased with temperature (30-65 °C), but this activity was higher in leaf (0.20 MCU/mL) compared with that in fruit and seed extracts (0.12 and 0.11 MCU/mL, respectively) at 50 °C. Proteolytic activity in the extracts assayed at different pH (2.5-12.0) suggested the presence of different types of active proteases, with maximum activity at acidic conditions (4.0-4.5). Inhibitory studies indicated that major activity in V. glabra extracts is related to cysteine proteases; however, the presence of serine, aspartic, and metalloproteases was also evident. The hydrolytic profile of caseins indicated that V. glabra leaves could be used as a rennet substitute in cheesemaking, representing a new and promising source of proteolytic enzymes.

The implication of metabolically active Vibrio spp. in the digestive tract of Litopenaeus vannamei for its post-larval development.

This work aimed to evaluate the link between the occurrence/abundance of Vibrio populations and bacterial composition in shrimp's intestine (Litopenaeus vannamei) during post-larval ontogenetic development and in its culture water, and the correlation of these with environmental parameters. The total and metabolically active populations of Vibrio in the digestive tract of shrimp during its post-larval development were analysed using quantitative PCR (qPCR) and reverse transcription qPCR targeting the 16S rRNA gene sequence. A lab-scale shrimp bioassay was performed for 80 days in a recirculating aquarium under strictly controlled conditions. The results indicate that the Vibrio population from shrimp's gut is associated with its developmental stage and the environment. Multivariate analyses revealed that the presence of Vibrio spp. drove the studied system, but their metabolically active performance was related to earlier developmental stages in an aqueous environment. Also, the samples taken from water of culture units to compare the influence of the aquatic environment on the intestinal microbial community during shrimp's ontogenetic development showed significant differences. Finally, our results revealed that Vibrio is an important member of shrimp's gut microbiota; however, its metabolic activity seems to be highly regulated, possibly by the host and by the rest of the microbiota.

Arabinoxylans and gelled arabinoxylans used as anti-obesogenic agents could protect the stability of intestinal microbiota of rats consuming high-fat diets.

This study evaluated the effect of using arabinoxylans (AX) and gelled arabinoxylans (AxGel) as anti-obesogenic agents on the faecal microbiota of rats fed with a high-fat (HF) diet. Results revealed that the HF content in diet caused obesity in rats and alterations in the taxonomic and functional profiles of faecal microbiota. However, these effects were lessened when AX and AxGel were used as ingredients of the HF diet. Metabolisms of amino acids and energy, as well as genetic information processing, were negatively affected when the rats consumed the HF diet; however, this effect was not observed if AX and AxGel were included as part of the diet formulation. Results suggest that AX may act as a prebiotic agent. Therefore, AX and AxGel could be considered as hypothetical protectors of the intestinal microbiota against HF consumption.

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences.

Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal (Phoca vitulina richardii) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway.

Functional metagenomics: a tool to gain knowledge for agronomic and veterinary sciences.

The increased global demand for food production has motivated agroindustries to increase their own levels of production. Scientific efforts have contributed to improving these production systems, aiding to solve problems and establishing novel conceptual views and sustainable alternatives to cope with the increasing demand. Although microorganisms are key players in biological systems and may drive certain desired responses toward food production, little is known about the microbial communities that constitute the microbiomes associated with agricultural and veterinary activities. Understanding the diversity, structure and in situ interactions of microbes, together with how these interactions occur within microbial communities and with respect to their environments (including hosts), constitutes a major challenge with an enormous relevance for agriculture and biotechnology. The emergence of high-throughput sequencing technologies, together with novel and more accessible bioinformatics tools, has allowed researchers to learn more about the functional potential and functional activity of these microbial communities. These tools constitute a relevant approach for understanding the metabolic processes that can occur or are currently occurring in a given system and for implementing novel strategies focused on solving production problems or improving sustainability. Several 'omics' sciences and their applications in agriculture are discussed in this review, and the usage of functional metagenomics is proposed to achieve substantial advances for food agroindustries and veterinary sciences.