Animal Gut Research Articles

Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture.

Bioflocs are microbial aggregates primarily composed of heterotrophic bacteria that play essential ecological roles in maintaining animal health, gut microbiota, and water quality in biofloc aquaculture systems. Despite the global adoption of biofloc aquaculture for shrimp and fish cultivation, our understanding of biofloc microbiota-particularly the dominant bacterial members and their ecological functions-remains limited. In this study, we employed integrated metataxonomic and metagenomic approaches to demonstrate that the family Rhodobacteraceae of Alphaproteobacteria consistently dominates the biofloc microbiota and plays essential ecological roles. We first analyzed a comprehensive metataxonomic dataset consisting of 200 16S rRNA gene amplicons collected across three Asian countries: South Korea, China, and Vietnam. Taxonomic investigation identified Rhodobacteraceae as the dominant and consistent bacterial members across the datasets. The predominance of this taxon was further validated through metagenomics approaches, including read taxonomy and read recruitment analyses. To explore the ecological roles of Rhodobacteraceae, we applied genome-centric metagenomics, reconstructing 45 metagenome-assembled genomes. Functional annotation of these genomes revealed that dominant Rhodobacteraceae genera, such as Marivita, Ruegeria, Dinoroseobacter, and Aliiroseovarius, are involved in vital ecological processes, including complex carbohydrate degradation, aerobic denitrification, assimilatory nitrate reduction, ammonium assimilation, and sulfur oxidation. Overall, our study reveals that the common practice of carbohydrate addition in biofloc aquaculture systems fosters the growth of specific heterotrophic bacterial communities, particularly Rhodobacteraceae. These bacteria contribute to maintaining water quality by removing toxic nitrogen and sulfur compounds and enhance animal health by colonizing gut microbiota and exerting probiotic effects.

Comparative gut microbiome research through the lens of ecology: theoretical considerations and best practices.

Comparative approaches in animal gut microbiome research have revealed patterns of phylosymbiosis, dietary and physiological convergences, and environment-host interactions. However, most large-scale comparative studies, especially those that are highly cited, have focused on mammals, and efforts to integrate comparative approaches with existing ecological frameworks are lacking. While mammals serve as useful model organisms, developing generalised principles of how animal gut microbiomes are shaped and how these microbiomes interact bidirectionally with host ecology and evolution requires a more complete sampling of the animal kingdom. Here, we provide an overview of what past comparative studies have taught us about the gut microbiome, and how community ecology theory may help resolve certain contradictions in comparative gut microbiome research. We explore whether certain hypotheses are supported across clades, and how the disproportionate focus on mammals has introduced potential bias into gut microbiome theory. We then introduce a methodological solution by which public gut microbiome data of understudied hosts can be compiled and analysed in a comparative context. Our aggregation and analysis of 179 studies shows that generating data sets with rich host diversity is possible with public data and that key gut microbes associated with mammals are widespread across the animal kingdom. We also show the effects that sample size and taxonomic rank have on comparative gut microbiome studies and that results of multivariate analyses can vary significantly with these two parameters. While challenges remain in developing a universal model of the animal gut microbiome, we show that existing ecological frameworks can help bring us one step closer to integrating the gut microbiome into animal ecology and evolution.

NpmC, a novel A1408 16S rRNA methyltransferase in the gut of humans and animals

16S rRNA methyltransferases that act on residue A1408, NpmA and NpmB, confer high-level resistance to virtually all the aminoglycosides, but their reports are scarce. Analysing metagenomic projects in a One Health context, we identified in human and animal gut microbiomes from China and Canada a novel gene, npmC, that shares an identity of 91.5% with npmA, and up to 92.7% at amino acidic level. The protein encoded by this gene presents the conserved motifs required for A1408 methylation. Expression of the gene resulted in high-level of resistance to 4,5-disubstituted 2-deoxystreptamine (2-DOS) and to 4-monosubstituted 2-DOS aminoglycosides, as well as a moderate resistance to 4,6-disusbstituted 2-DOS aminoglycosides, including the last resort aminoglycoside plazomicin. Methylation at residue A1408 was further confirmed by mass spectrometry assays. The analysis of the npmC gene background revealed that its genetic context is associated to different insertion sequences that could mobilise it. Similarities in the genetic context between npmC and npmA suggest that they share a common ancestor. The immediate genetic context of this methyltransferase suggests high relationship to the Eubacteriales order. This finding enlarges the list of the true pan-aminoglycoside 16S rRNA methyltransferases, that threaten the usefulness and development of next-generation aminoglycosides.

Metagenomics and selective culture reveal the major transfer and prevalence of antibiotic resistance genes in Tibetan Plateau animals

The Tibetan Plateau, despite being the highest and least populated plateau on the Earth, harbors antibiotic-resistant bacteria (ARBs) as well as antibiotic resistance genes (ARGs) in its pristine environment and animals. There is, however, limited knowledge regarding antibiotic resistance in Tibetan Plateau animals. Here, fecal samples of grazing yaks and intestinal content samples of wild rats were collected at altitudes of 2920m and 4360m and subjected to selective culture, PCR, and metagenomic sequencing. The results revealed a higher antibiotic resistance rate in low-altitude regions than in high-altitude regions. The simultaneous presence of bacteria exhibiting different antibiotic resistance phenotypes across multiple samples suggests the potential emergence of multidrug-resistant strains within the animal gut microbiota. Pseudomonas spp. and Escherichia coli were the predominant ARBs. In contrast to low-altitude regions with frequent human activities, ARG dissemination in the Tibetan Plateau did not show a significant correlation with mobile genetic elements. ARGs in high-altitude regions relied more on vertical gene transmission. This study expands our knowledge of antibiotic resistance in grazing and wild animals inhabiting the Tibetan Plateau, thereby highlighting the potential threat posed by antibiotic resistance in this region.

Altitude shapes gut microbiome composition accounting for diet, thyroid hormone levels, and host genetics in a subterranean blind mole rat

The animal gut microbiome acts as a crucial link between the host and its environment, playing a vital role in digestion, metabolism, physiology, and fitness. Using 16S rRNA metabarcoding, we investigated the effect of altitude on the microbiome composition of Anatolian Blind Mole Rats (Nannospalax xanthodon) across six locations and three altitudinal groups. We also factored in the host diet, as well as host microsatellite genotypes and thyroid hormone levels. The altitude had a major effect on microbiome composition, with notable differences in the relative abundance of several bacterial taxa across elevations. Contrary to prior research, we found no significant difference in strictly anaerobic bacteria abundance among altitudinal groups, though facultatively anaerobic bacteria were more prevalent at higher altitudes. Microbiome alpha diversity peaked at mid-altitude, comprising elements from both low and high elevations. The beta diversity showed significant association with the altitude. Altitude had a significant effect on the diet composition but not on its alpha diversity. No distinct altitude-related genetic structure was evident among the host populations, and no correlation was revealed between the host genetic relatedness and microbiome composition nor between the host microbiome and the diet. Free thyroxine (FT4) levels increased almost linearly with the altitude but none of the bacterial ASVs were found to be specifically associated with hormone levels. Total thyroxine (TT4) levels correlated positively with microbiome diversity. Although we detected correlation between certain components of the thyroid hormone levels and the microbiome beta diversity, the pattern of their relationship remains inconclusive.

Comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.

The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g., differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the "One Health" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.

Microscale sampling of the coral gastrovascular cavity reveals a gut-like microbial community

Animal guts contain numerous microbes, which are critical for nutrient assimilation and pathogen defence. While corals and other Cnidaria lack a true differentiated gut, they possess semi-enclosed gastrovascular cavities (GVCs), where vital processes such as digestion, reproduction and symbiotic exchanges take place. The microbiome harboured in GVCs is therefore likely key to holobiont fitness, but remains severely understudied due to challenges of working in these small compartments. Here, we developed minimally invasive methodologies to sample the GVC of coral polyps and characterise the microbial communities harboured within. We used glass capillaries, low dead volume microneedles, or nylon microswabs to sample the gastrovascular microbiome of individual polyps from six species of corals, then applied low-input DNA extraction to characterise the microbial communities from these microliter volume samples. Microsensor measurements of GVCs revealed anoxic or hypoxic micro-niches, which persist even under prolonged illumination with saturating irradiance. These niches harboured microbial communities enriched in putatively microaerophilic or facultatively anaerobic taxa, such as Epsilonproteobacteria. Some core taxa found in the GVC of Lobophyllia hemprichii from the Great Barrier Reef were also detected in conspecific colonies held in aquaria, indicating that these associations are unlikely to be transient. Our findings suggest that the coral GVC is chemically and microbiologically similar to the gut of higher Metazoa. Given the importance of gut microbiomes in mediating animal health, harnessing the coral “gut microbiome” may foster novel active interventions aimed at increasing the resilience of coral reefs to the climate crisis.

Promotion of antibiotic-resistant genes dissemination by the micro/nanoplastics in the gut of snail Achatina fulica

Terrestrial animal intestines are hotspots for the enrichment of micro/nano plastics (M/NPs) and antibiotic-resistant genes (ARGs). However, little is known about the further impact of M/NPs on the spread of ARGs in animal guts. This study investigates the role of M/NPs (polystyrene) with varying particle sizes (0.082, 42, and 182 μm), concentrations (10 and 100 mg/L), and exposure durations (4 and 16 days) in the ARGs dissemination via conjugation in the edible snail (Achatina fulica) gut. Combination of qPCR with 16S rRNA-based sequencing, we found that PS exposure caused intestinal cell impairment and shifts in the gut microbial community of snails. Conjugation rate increased with PS particle sizes in the snail gut. After 4 days of exposure, significantly higher conjugation rates were observed in the gut exposed to 100 mg/L PS compared to 10 mg/L, however, this trend reversed after 16 days. Consistently, the abundances of conjugation relevant genes trfA and trbB shared similar trends to the conjugation ratios in the snail gut after PS exposure. Transconjugant diversity was much lower in 10 mg/L PS groups than in 100 mg/L PS treatments. Therefore, this study suggests that the presence of M/NPs would complicate management of ARG spread. The selection pressure exerted by M/NPs may sustain or even amplify the spread of ARGs in the gut of terrestrial animals even in the absence of antibiotics. It highlights the necessity of avoiding M/NPs intake as a part of comprehensive strategy for cubing ARG dissemination in the gut of animals.

Effects of cadmium on the intestinal health of the snail Bradybaena ravida Benson.

The heavy metal cadmium (Cd) is a toxic and bioaccumulative metal that can be enriched in the tissues and organs of living organisms through the digestive tract. However, more research is needed to determine whether food-sourced Cd affects the homeostasis of host gut microflora. In this study, the snail Bradybaena ravida (Benson) was used as a model organism fed with mulberry leaves spiked with different concentrations of Cd (0, 0.052, 0.71, and 1.94 mg kg-1). By combining 16S rRNA high-throughput sequencing with biochemical characterization, it was found that there were increases in the overall microbial diversity and abundances of pathogenic bacteria such as Corynebacterium, Enterococcus, Aeromonas, and Rickettsia in the gut of B. ravida after exposure to Cd. However, the abundances of potential Cd-resistant microbes in the host's gut, including Sphingobacterium, Lactococcus, and Chryseobacterium, decreased with increasing Cd concentrations in the mulberry leaves. In addition, there was a significant reduction in activities of energy, nutrient metabolism, and antioxidant enzymes for gut microbiota of snails treated with high concentrations of Cd compared to those with low ones. These findings highlight the interaction of snail gut microbiota with Cd exposure, indicating the potential role of terrestrial animal gut microbiota in environmental monitoring through rapid recognition and response to environmental pollution.

The Role of Geography, Diet, and Host Phylogeny on the Gut Microbiome in the Hawaiian Honeycreeper Radiation.

The animal gut microbiome can have a strong influence on the health, fitness, and behavior of its hosts. The composition of the gut microbial community can be influenced by factors such as diet, environment, and evolutionary history (phylosymbiosis). However, the relative influence of these factors is unknown in most bird species. Furthermore, phylosymbiosis studies have largely focused on clades that diverged tens of millions of years ago, and little is known about the degree of gut microbiome divergence in more recent species radiations. This study explores the drivers of microbiome variation across the unique and recent Hawaiian honeycreeper radiation (Fringillidae: Drepanidinae). Fecal samples were collected from 14 extant species spanning the main islands of the Hawaiian archipelago and were sequenced using three metabarcoding markers to characterize the gut microbiome, invertebrate diet, and plant diet of Hawaiian honeycreepers. We then used these metabarcoding data and the honeycreeper host phylogeny to evaluate their relative roles in shaping the gut microbiome. Microbiome variation across birds was highly individualized; however, source island had a small but significant effect on microbiome structure. The microbiomes did not recapitulate the host phylogenetic tree, indicating that evolutionary history does not strongly influence microbiome structure in the honeycreeper clade. These results expand our understanding of the roles of diet, geography, and phylogeny on avian microbiome structure, while also providing important ecological information about the diet and gut microbiota of wild Hawaiian honeycreepers.

Effects of Bifidobacterium-Fermented Milk on Obesity: Improved Lipid Metabolism through Suppression of Lipogenesis and Enhanced Muscle Metabolism.

Obesity is a major global health concern. Studies suggest that the gut microflora may play a role in protecting against obesity. Probiotics, including lactic acid bacteria and Bifidobacterium, have garnered attention for their potential in obesity prevention. However, the effects of Bifidobacterium-fermented products on obesity have not been thoroughly elucidated. Bifidobacterium, which exists in the gut of animals, is known to enhance lipid metabolism. During fermentation, it produces acetic acid, which has been reported to improve glucose tolerance and insulin resistance, and exhibit anti-obesity and anti-diabetic effects. Functional foods have been very popular around the world, and fermented milk is a good candidate for enrichment with probiotics. In this study, we aim to evaluate the beneficial effects of milks fermented with Bifidobacterium strains on energy metabolism and obesity prevention. Three Bifidobacterium strains (Bif-15, Bif-30, and Bif-39), isolated from newborn human feces, were assessed for their acetic acid production and viability in milk. These strains were used to ferment milk. Otsuka-Long-Evans Tokushima Fatty (OLETF) rats administered Bif-15-fermented milk showed significantly lower weight gain compared to those in the water group. The phosphorylation of AMPK was increased and the expression of lipogenic genes was suppressed in the liver of rats given Bif-15-fermented milk. Additionally, gene expression related to respiratory metabolism was significantly increased in the soleus muscle of rats given Bif-15-fermented milk. These findings suggest that milk fermented with the Bifidobacterium strain Bif-15 can improve lipid metabolism and suppress obesity.

40 The gut microbiota modifies host-parasite interactions

Abstract It is well documented that parasitic infections induce a profound change in the structure and function of host gut microbiota, likely due to infection-associated perturbations in the gut microenvironment. However, the mechanisms remain largely unknown. Here we aim to understand how the gut microbiota is modified by host-parasite relationships or vice versa using an integrated multi-omics analysis in a swine-Ascaris infection model. Female pigs (n = 30; 6 to 8 mo of age) were randomly divided into three groups (n = 10 per group). One group served as normal uninfected controls (NU); the remaining 20 pigs were inoculated per os with ~10,000 infective A. suum eggs; and the infection was allowed to progress for 35 d post-inoculation (dpi). At 21 dpi, one of the infected groups (IP) was treated with a single daily dose of an anthelmintic drug, Panacur, for three consecutive days while the other infected pigs remained untreated (IU). At necropsy, intestine tissue, serum and fecal samples were collected for untargeted metabolome analysis using UPLC-MS/MS and the fecal microbiota was characterized using full-length 16S rRNA gene-based sequencing with DADA2. Fecal and serum metabolites were categorized for their origin using MetOrigin. An integrated multi-omics analysis was performed using DIABLO algorithms and NetCoMi networking tools. Our results showed that A. suum worms were well developed in pigs from the IU group, which harbored a significantly reduced microbiota alpha diversity (Simpson, P < 0.005) compared with NU. The infection altered the abundance of at least 17 bacterial species/strains, including multiple butyrate-producing Clostridium spp., such as C. butyricum. The infection also dysregulated 51 fecal metabolites, including microbiota-derived metabolites such as glutaric acid and p-Cresol sulfate, and succinate of mixed origin. Moreover, the anthelmintic treatment was efficacious and eliminated all worms from the gut. Nevertheless, 11 pathways of both host and microbiota origin were significantly enriched in the gut of pigs from the IP group, including peptidoglycan biosynthesis, histidine metabolism (in both feces and serum), and primary bile acid biosynthesis, suggesting the infection-induced alterations may not be transient. In conclusion, the host microbiota modified swine-Ascaris interactions via three different mechanisms. First, microbiota-derived metabolites directly regulate host gene expression, which in turn affects host physiology and immune responses. Second, plasticity of the gut microbiota allows the exploitation of the niche differentiated upon infection, resulting in blossom of certain strains in the gut of post-treated animals. Lastly, the host microbiota is likely one of the key determinants of parasite gut microbiota, indirectly exerting its effect on parasite physiology and nutrition. Further studies aiming to understand reciprocal yet complex relations between the gut microbiota, the host, and parasites (including parasite gut microbiota) will be conducive to the design of next-generation functional anthelmintics.

Opportunistic Features of Non-Clostridium botulinum Strains Containing bont Gene Cluster.

The cluster of genes determining the production of botulinum toxins is an attribute of not only the Clostridium botulinum species. This cluster is also found in other members of the Clostridium genus, such as C. baratii, C. butyricum, and C. sporogenes. The occurrence of a botulinum-like cluster has also been recorded in strains of other genera, i.e., Enterococcus faecium, as well as in a Gram-negative species isolated from freshwater sediments; however, the biological activity of bont-related genes has not been noted. It can be said that the mentioned species have a dual nature. Another species with a dual nature is C. butyricum. This bacterium is a common human and animal gut commensal bacterium and is also frequently found in the environment. Although non-toxigenic strains are currently used as probiotics in Asia, other strains have been implicated in pathological conditions, such as botulism in infants or necrotizing enterocolitis in preterm neonates. Additionally, C. baratii strains are rare opportunistic pathogens associated with botulism intoxication. They have been isolated from food and soil and can be carried asymptomatically or cause botulism outbreaks in animals and humans. In addition to the mentioned clostridia, the other microorganisms considered as non-toxigenic have also been suspected of carrying botulinum cluster Gram-negative bacteria, such as Chryseobacterium piperi isolated from freshwater sediments; however, the biological activity of bont-related genes has not been noted. Additionally, Enterococcus faecium strains have been discovered carrying BoNT-related clusters (BoNT/En). Literature data regarding the heterogeneity of BoNT-producing strains indicate the requirement to reclassify C. botulinum species and other microorganisms able to produce BoNTs or possess botulinum-like gene clusters. This article aims to show the dual nature of Clostridium strains not belonging to the C. botulinum species that are sporadically able to carry bont clusters, which are usually considered saprophytic and even probiotic, and bont-like clusters in microorganisms from other genera. The aim was also to consider the genetic mechanisms of botulinum cluster expression in strains that are considered opportunistic and the microbiological safety aspects associated with their occurrence in the environment.

Subtle changes in plant diversity in the Bavarian Alps over the past eight decades.

Historical resurveys represent a unique opportunity to analyze vegetation dynamics over longer timescales than is typically achievable. Leveraging the oldest historical dataset of vegetation change in the Bavarian Alps, Germany, we address how environmental conditions, vegetation composition, and functional diversity in the calcareous grasslands of the Schachen region have changed across different elevational ranges over an 83-year timeframe. We document changes in regional average temperature and precipitation. We use indicator values (IV) for species' ecological preferences and their palatability to grazers to infer local conditions (temperature, soil moisture/fertility, and grazing regime). We further estimate changes in temporal beta-diversity and functional trait community composition between historical (1936) and contemporary (2019) surveys in two elevational (subalpine and alpine) belts. Both subalpine and alpine sites became drier; subalpine sites also became warmer with more palatable plants. Species occurrence and abundance in the Schachen region has not changed substantially over time despite changing macroclimate and local environmental conditions under anthropogenic change. Yet these grasslands have experienced several "invisible" changes in functional composition over the past 80 years. As the Schachen has become drier, species with traits related to drought tolerance and animal-based dispersal have increased in dominance. Specifically, in alpine sites, community-weighted means revealed that with low fecundity, higher potential for endo- and epizoochory (seed dispersal via animal gut and fur, respectively), higher foliar frost tolerance, and deeper dormancy increased in dominance. Similar trends were found for increasing dominance of low fecundity, epizoochorous species in subalpine sites. Vegetation data from resurveying historical plots in combination with changes in local conditions, classic biodiversity indices, and functional trait indices can provide more holistic insights into changes in the environment and potential impacts of those environmental changes on long-term plant community and functional diversity.

Host diet drives gut microbiome convergence between coral reef fishes and mammals.

Animal gut microbiomes are critical to host physiology and fitness. The gut microbiomes of fishes-the most abundant and diverse vertebrate clade-have received little attention relative to other clades. Coral reef fishes, in particular, make up a wide range of evolutionary histories and feeding ecologies that are likely associated with gut microbiome diversity. The repeated evolution of herbivory in fishes and mammals also allows us to examine microbiome similarity in relationship to diet across the entire vertebrate tree of life. Here, we generate a large coral reef fish gut microbiome dataset (n = 499 samples, 19 species) and combine it with a diverse aggregation of public microbiome data (n = 447) to show that host diet drives significant convergence between coral reef fish and mammalian gut microbiomes. We demonstrate that this similarity is largely driven by carnivory and herbivory and that herbivorous and carnivorous hosts exhibit distinct microbial compositions across fish and mammals. We also show that fish and mammal gut microbiomes share prominent microbial taxa, including Ruminoccocus spp. and Akkermansia spp., and predicted metabolic pathways. Despite the major evolutionary and ecological differences between fishes and mammals, our results reveal that their gut microbiomes undergo similar dietary selective pressures. Thus, diet, in addition to phylosymbiosis must be considered even when comparing the gut microbiomes of distantly related hosts.

Synbiotic supplementation with xylooligosaccharide derived probiotic Lactobacillus gasseri and prebiotic mixture exerts antidiabetic effects via collaborative action

The guts of young humans and animals are abundant in various beneficial bacteria, and certain probiotics have a remarkable blood glucose-regulating impact on diabetic mice. This study adopts a novel approach based on the separation and purification after prebiotics enrich probiotics entering the stable stage to explore synbiotics, which is more rapid and circumvents difficulties such as difficult intestinal entry, long time consumption, and challenges in finding matching synbiotics. Through measuring the inhibitory activity on α-glucosidase and α-amylase in vitro and its probiotic characteristics, Lactobacillus gasseri Y11 is screened and identified. Utilizing a high-fat diet combined with streptozotocin to establish a diabetic mouse model, the hypoglycemic mechanism of synbiotics in type 2 diabetic mice is investigated. The association between the gut microbiota and serum indices and genes is analyzed using the Mantel test and Spearman correlation analysis. The findings indicate that different intervention groups can ameliorate body weight and HDL-C, and reduce FBG, TG, TC, LDL-C, HbA1C, INS, HOMA-IR, and QUICK1 levels, enhancing blood glucose homeostasis, blood lipid levels, and insulin sensitivity of mice, and regulating the expression of genes like GIP, GLP-1, PPARγ, PEPCK, G6PASE, MTOR-S6K1, and GLUT-2 in the ileum and liver. Additionally, 16S rRNA gene sequencing is employed to analyze the gut microbiota. In the Synbiotics group, the relative abundance of Bifidobacterium and Akkermansia is increased. In summary, this study devises a new synbiotics screening strategy, explores its potential in treating type 2 diabetes, and provides a new research direction for the anti-diabetic mechanism.

Nickel and Soil Fertility: Review of Benefits to Environment and Food Security

Nickel (Ni) is an essential micronutrient for plants, responsible for metabolizing urea nitrogen (urea-N) by urease and mitigating abiotic and oxidative stresses through the glyoxalase (Gly) and glutathione (GSH) cycles. However, excess Ni is toxic to flora at >100 mg kg−1, except for hyperaccumulators that tolerate >1000 mg kg−1 Ni. This review discusses the benefits of Ni nutrient management for soil fertility, improving food security, and minimizing adverse environmental impacts from urea overapplication. Many farming soils are Ni deficient, suggesting that applying 0.05–5 kg ha−1 of Ni improves yield and urea-N use efficiency. Applied foliar and soil Ni fertilizers decrease biotic stresses primarily by control of fungal diseases. The bioavailability of Ni is the limiting factor for urease synthesis in plants, animal guts, and the soil microbiome. Improved urease activity in plants and subsequently through feed in livestock guts reduces the release of nitrous oxide and nitrite pollutants. Fertilizer Ni applied to crops is dispersed in vegetative tissue since Ni is highly mobile in plants and is not accumulated in fruit or leafy tissues to cause health concerns for consumers. New methods for micronutrient delivery, including rhizophagy, recycled struvite, and nanoparticle fertilizers, can improve Ni bioavailability in farming systems.

Effects of wheat-based fermented liquid feed on growth performance, nutrient digestibility, gut microbiota, intestinal morphology, and barrier function in grower-finisher pigs.

Fermented liquid feed (FLF) can improve dietary nutrient absorption levels, degrade anti-nutrient factors in diets, and increase beneficial bacteria abundance in animal guts. However, few systematic studies have been conducted on WFLF in pigs. The present study evaluates the effects of WFLF on the growth performance, nutrient digestibility, gastric volume, intestinal morphology, intestinal health, intestinal barrier function, serum biochemical immunity, gut microbiota, and intestinal microbial diversity of grower-finisher pigs. In total, 80 weaned pigs were randomly allocated to two treatment groups based on their initial body weight: a basal diet with pellet dry feeding (CON) and a basal diet with wheat-based fermented liquid feed (WFLF), with four replicate pens per group. The experiment lasted 82 d. Compared with CON pigs, those fed WFLF were heavier significantly at 60-82 d and had significantly higher average daily feed intake, average daily gain, and gain: feed ratio at 60-82 d and 1-82 d. WFLF pigs had significantly greater jejunum, total tract, and ileal digestibility for all nutrients and amino acids, excluding arginine, than CON pigs. WFLF intake influenced villus height, villus height: crypt depth ratio of the anterior segment of the jejunum(A-jejunum), crypt depth, and redox potential of the posterior segment of the jejunum (P-jejunum) while significantly affecting body weight. Additionally, FLF improved gastric capacity significantly. Furthermore, mRNA expression of occludin and claudin-1 in the mucosa of the ileum and jejunum was significantly higher in WFLF pigs than in CON pigs. WFLF increased serum concentrations of alanine transaminase and reduced low-density lipoprotein cholesterol, total cholesterol, and total bile acid content. The alpha diversity (Shannon and Simpson indices) in the stomachs of WFLF pigs was significantly higher than in CON pigs. Microbial diversity in the stomach, ileum, and cecum, as well as the abundance of lactic acid bacteria, were increased in WFLF pigs compared to CON pigs. In conclusion, WFLF intake may positively influence intestinal ecology by improving digestive tract structure, upregulating intestinal barrier-related genes, and improving intestinal morphology to enhance intestinal digestive function and health. Collectively, the present study shows that WFLF intake can increase growth performance while maintaining beneficial nutrient digestibility in grower-finisher pigs.

Effects of Tibetan Sheep-Derived Compound Probiotics on Growth Performance, Immune Function, Intestinal Tissue Morphology, and Intestinal Microbiota in Mice.

Probiotics play an important role in animal growth, immunity, and gut microbial balance and are now widely used in agriculture, food, and medicine. This study analysed the effects of different concentrations of Tibetan sheep compound probiotics on the immunity, tissue morphology, and intestinal microbiota of mice using histological, molecular, and 16S rRNA techniques. The results showed that the composite probiotics sourced from Tibetan sheep improved the growth performance of mice, increased the length of small intestinal villi and mucosal thickness, and enhanced the intestinal barrier function of mice. DZ-L and DZ-M significantly increased the mRNA expression levels of ZO-1, Occludin, and Claudin-1 mRNA. They also up-regulated IL-10 and TNF-β, and down-regulated TNF-α, IL-1β, and IL-8. The immune function of mice was enhanced, with DZ-M treatment having an extremely significant effect, while the effect of DZ-H treatment was slightly lower compared to DZ-L and DZ-M. In addition, the composition and diversity of the intestinal microbiota were modulated, and at the phylum level, the relative abundance of Firmicutes was higher in the DZ-M group, the relative abundance of Desulfobacterota, Actinobacteriota, and Patescibacteria was reduced in the probiotic complex group, and the relative abundance of Verrucomicrobiota was higher. At the genus level, the relative abundance of Muribaculaceae was higher in the DZ-L and DZ-M groups, and the relative abundance of Lachnospiraceae_NK4A136_group in the DZ-H group; and the relative abundance of Bacteroides and Roseburia in the composite probiotic group. This study can improve the reference for the development of new green feed additives instead of antibiotics, which will also further promote the development of the livestock industry.

A decade of advances in black soldier fly research: from genetics to sustainability

Abstract Black soldier fly (BSF), Hermetia illucens, is one of the most explored insect species mass-produced for feed, but also for food and technical purposes. Considering the rapid developments in both research and industrial production of this insect species in the last decade, this review intends to reflect on the most current scientific insights and define the future trends and needs for the most relevant associated research fields. The review reflects on the aspects of BSF production and reproduction, utilization of BSF biomass as components of animals’ feeds and human food. It also provides reflection on genetics, microbiology and sustainability. The analysis identifies the need in future research associated with compositions of fungal and viral communities of insects and their environments and mapping the dynamics of BSF gut physiology and microbiota in varying conditions. High interest will be devoted to establishing genomic resources, to characterize genotypic diversity, and to harness its potential through selective breeding to improve BSF performance quantitatively and/or qualitatively. Further research will follow on the use of BSF for food and feed development, potentially for specific application cases, associated with animal gut microbiome improvement and antimicrobial properties of BSF biomass. The further in-depth exploration of the potential of BSF for waste biotransformation and the assessment of its circularity potential are also expected to be major focus points of research in the next decade.