Animal microbiome最新文献

Background: High-throughput sequencing technologies play an increasingly active role in the surveillance of major global health challenges, such as the emergence of antimicrobial resistance. The post-weaning period is of critical importance for the swine industry and antimicrobials are still required when infection occurs during this period. Here, two sequencing approaches, shotgun metagenomics and metatranscriptomics, have been applied to decipher the effect of different treatments used in post-weaning diarrhea on the transcriptome and resistome of pig gut microbiome. With this objective, a metagenome-assembled genome (MAG) catalogue was generated to use as a reference database for transcript mapping obtained from a total of 140 pig fecal samples in a cross-sectional and longitudinal design to study differential gene expression. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, gentamicin, and amoxicillin, and an oral commercial vaccine, a control with water acidification, and an untreated control. For metatranscriptomics, fecal samples from pigs were selected before weaning, three days and four weeks post-treatment.

Results: The final non-redundant MAGs collection comprised a total of 1396 genomes obtained from single assemblies and co-assemblies per treatment group and sampling time from the metagenomics data. Analysis of antimicrobial resistance genes (ARGs) at this assembly level considerably reduced the total number of ARGs identified in comparison to those found at the reads level. Besides, from the metatranscriptomics data, half of those ARGs were detected transcriptionally active in all treatment groups. Differential gene expression between sampling times after treatment found major number of differential expressed genes (DEGs) against the group treated continuously with amoxicillin, with DEGs being correlated with antimicrobial resistance. Moreover, at three days post-treatment, a high number of significantly downregulated genes was detected in the group treated with gentamicin. At this sampling time, this group showed an altered expression of ribosomal-related genes, demonstrating the rapid effect of gentamicin to inhibit bacterial protein synthesis.

Conclusions: Different antimicrobial treatments can impact differently the transcriptome and resistome of microbial communities, highlighting the relevance of novel sequencing approaches to monitor the resistome and contribute to a more efficient antimicrobial stewardship.

Background: Aquaculture is one of the fastest growing sectors of food production and covers more than half of the market demand for fish and fishery products. However, aquaculture itself faces numerous challenges, such as infectious disease outbreaks, which are one of the limiting factors for the growth and environmental sustainability of modern aquaculture. Understanding the composition and diversity of the gut microbiota of fish is important to elucidate its role in host health and aquaculture management. In addition, the gut microbiota represents a valuable source of bacteria with probiotic potential for farmed fish.

Results: In this study, we analysed the intestinal microbiota of two economically important fish species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), using 16S rRNA gene amplicon sequencing. The taxonomic analysis identified 462 amplicon sequence variants at a similarity level of 99 and showed similar alpha diversity indices between seabass and gilthead seabream. Beta diversity analysis showed no significant differentiation in gut microbiota between fish species or aquaculture sites. Among the culturable isolates, a high proportion of Photobacterium damselae and Bacillus spp. was detected. We selected a single Bacillus velezensis isolate and further characterised its biosynthetic potential by performing whole genome sequencing. Its genome contains biosynthetic gene clusters for most of the common secondary metabolites typical of B. velezensis. Antibiotic susceptibility testing showed the sensitivity of the selected isolates to several antibiotics according to EFSA recommendations. Furthermore, stimulation of peripheral blood leukocytes (PBL) with B. velezensis resulted in a strong pro-inflammatory response, with a pronounced upregulation of cytokines il1b, il6, tnfa and il10 observed over time.

Conclusions: Overall, this study provides an insight into the composition of the intestinal microbiota and the diversity of culturable intestinal bacteria of two economically most important fish species from Adriatic cage culture and sheds light on the autochthonous intestinal B. velezensis as a promising probiotic candidate for Mediterranean aquaculture.

Background: The parasite Hematodinium sp. causes morbidity and seasonal mortality events in more than 40 decapod species globally and therefore, it is now recognised as a significant threat to the future sustainability of shellfish fisheries and aquaculture worldwide. Among these, Norway lobster (Nephrops norvegicus), an important representative of the marine benthos and supporting the most valuable shellfish fishery in the UK, experience yearly seasonal Hematodinium sp. patent infections. Currently, little is known about the N. norvegicus microbiome and potential role during Hematodinium sp.

Infection: Therefore, in this study we investigated the microbiome dynamics of N. norvegicus associated with Hematodinium sp. infection and disease progression in the haemolymph and gut. N. norvegicus were sampled from the Clyde Sea Area, Scotland during the peak of the Hematodinium sp. patent infection. The presence and intensity of Hematodinium sp. infection were determined using the body colour method (BCM), pleopod method (PM), histology (heart, gonads, hepatopancreas, gills and muscle) and molecular tools (PCR).

Results: Marked shifts in the bacterial richness of the haemolymph and significant alterations in the overall bacterial community composition of both tissues were observed in infected lobsters. These changes, observed even at subpatent levels of infection (only positive by PCR), indicate a prompt and persistent microbiome shift associated with Hematodinium sp.

Infection: Furthermore, smaller healthy animals (25.2 ± 1.20 mm CL) known to be particularly susceptible to high severity infection displayed a decreased microbiome richness in the haemolymph suggesting a potential link between the host microbiome and susceptibility to disease progression, a possibility that merits further research.

Conclusions: This study offers the first insights into the pathobiome of N. norvegicus due to Hematodinium sp. infection and disease that in turn provides a foundation for further studies on the pathogenesis of this important parasitic disease.

Background: Sirtuins are deacetylases that are highly conserved throughout the animal kingdom. They act as metabolic sensors that coordinate cellular responses, allowing an adapted response to various stressors. Epithelial cells, especially those of the intestine, are directly exposed to a wide range of stressors. Together with the microbiota, they form a complex ecosystem with mutual influences. The significance of sirtuins in this complex system is still waiting to be clarified.

Results: Here, we show that a protein-restricted diet strongly increases the intestinal expression of sirtuin 4 (dSirt4), the only mitochondrial sirtuin in Drosophila. To elucidate the effects of deregulated dSirt4 expression in the intestine, we analyzed dSirt4 knockout flies. These flies showed substantial changes in their intestinal proteome and physiological properties. One of the most striking effects was the strong induction of lysozymes in the intestine, with a corresponding increase in lysozyme activity. This effect was organ-autonomous, as it was also observed in flies with dSirt4 knocked out only in intestinal enterocytes. The significant increase in lysozyme abundance in response to tissue-specific dSirt4 knockdown did not reduce the total number of bacteria in the intestine. However, it did affect the microbiota composition by reducing the number of gram-positive bacteria. This effect on microbiota composition can be attributed to dSirt4-dependent lysozyme expression, which is absent in a lysozyme-deficient background. dSirt4 knockout in the enterocytes shortened the lifespan of the flies, as did ectopic lysozyme overexpression in the enterocytes.

Conclusions: The only mitochondrial sirtuin in Drosophila, dSirt4, is induced by dietary stress in intestinal epithelial cells, which directly regulates the lysozyme activity of these cells. We could associate this altered lysozyme activity with a shift in the microbiota composition, demonstrating a direct link between stress, nutrition, and the host's microbiota regulation.

Background: Inonotus obliquus is a medicinal edible fungus that contains a variety of biologically active ingredients and has multiple physiological effects. When supplemented in avian diet, Inonotus obliquus has proved to be beneficial. However, information regarding these effects on mammals is scanty. The present study aims to investigate the effect of supplementation of Inonotus obliquus fermentation product (IOFP) on the growth performance, antioxidant capacity, meat quality, intestinal function and gut microbiota of rabbit exploratorily, which may act as an important feed additive and also as an antibiotic alternative with its medicinal properties.

Results: Dietary supplementation of IOFP increased body weight (P < 0.01) at the initial 21 d and improved feed efficiency throughout the 35 d experimental period when compared to control group. At the same time it was observed that meat quality and carcass parameters improved upon supplementation of IOFP. Additionally, IOFP supplementation resulted in significant increases (P < 0.05) in total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and nitric oxide (NO) activity or concentration in the serum and muscle. The crypt depth decreased significantly, whereas the villus height/crypt depth (V/C) value increased (P < 0.05). The concentration of secrete IgA (sIgA) of the intestine also increased (P < 0.05). IOFP supplementation significantly increased the fold change expression of Claudin 1, Occludin, ZO1, and ZO2 (P < 0.05) when compared to the respective gene expression levels of the duodenum and jejunum tissues of control group. Further study on cecum microbiota revealed that IOFP supplementation increased the microbiota diversity by increasing the number of beneficial bacteria and reducing the numbers of pathological bacteria. It was observed that cecum metabolites produced in the treated group were related to antioxidants, antiinflammation and antidepressive effects. The harmful metabolites related to fat deposition, loss of appetite and cytotoxic conditions decreased. Pearson's correlation studies between different bacteria and metabolites revealed that the metabolites produced were regulated by the beneficial and harmful bacteria respectively.

Conclusions: IOFP enhanced intestinal morphology and function, and organismic antioxidant capacity, probably by increasing the concentration of beneficial microbiota and metabolites resulting in improvement of body weight, feed efficiency, and parameters related to meat quality and carcass traits of rabbits.

Hyperketonemia (HYK) is characterized by elevated levels of blood ketone bodies in dairy cows. Despite previous research on the physiological events related to HYK, associations between the rumen metagenome, metabolome, and HYK have not been well described. Therefore, the objective of this study was to compare rumen metagenome and metabolome profiles of cows with naturally occurring HYK to those without HYK during the first two weeks postpartum. Blood beta-hydroxybutyrate (BHB) concentrations at d 5, 10 and 14 postpartum were used to classify 16 rumen cannulated Holstein cows as either hyperketonemic (+ HYK; ≥1.2 mmol/L BHB at any of the collection days) or non-hyperketonemic (-HYK). Five + HYK cows were identified and were paired with 5 -HYK cows based on parity and calving date. Microbial DNA was extracted from rumen fluid and sequenced using shotgun metagenomics with the Illumina platform. Kraken2 was used to map reads to microbial taxonomic groups and Humann3.8 was used to predict potential functions. Metabolome profiling of rumen fluid was conducted using high-resolution liquid chromatography-mass spectroscopy. MetaboAnalyst6.0 was used to identify potential changes in metabolic pathways. Metagenomes and metabolomes comparisons were conducted using mixed models that included the fixed effects of group, day, their interaction, and the random effect of cow. There was minimal difference detected in alpha diversity for the metagenome, but differences in the metabolome were detected by HYK status. The concentration of asparagine and p-cresol was greater in + HYK cows compared to -HYK, but citrulline was greater in -HYK cows throughout all days considered. On d5 the concentration of ornithine was greater in + HYK compared to-HYK cows, and on d10 acetate was greater in the -HYK cows. There were no differences detected in the pathway analysis from the metabolites quantified by HYK status. Overall, modest differences in rumen metabolome were observed between + HYK and -HYK cows in early lactation. Future studies should explore associations between the rumen environment and HYK as this could be informative for treatment and management practices.

The gut microbiome plays a crucial role in intestinal maturation, metabolism, and immunoregulation, significantly influencing the host's health and growth performance. This review highlights the use of metagenomic techniques to the composition, function, and dynamic changes of the pig gut microbiota. Research has revealed that environmental and host factors, particularly diet, drive significant variations in microbial composition, which in turn shape host epigenetics through microbial components and metabolites. Furthermore, the strong correlation between the gut microbiota and host health presents opportunities for improving growth performance in the livestock industry.

Infectious bovine keratoconjunctivitis (IBK), or pinkeye, represents a significant economic challenge to dairy and beef cattle industries resulting in decreased productivity and increased treatment costs. The current IBK prevention and control strategies in cattle face challenges owing to the multifactorial nature of the disease, the rise of antibiotic resistance in IBK pathogens, and inconsistent efficacy of IBK vaccines. Recent efforts in metagenomic characterization of the eye microbiome in humans and animals, including cattle, have revealed that the ocular surface is colonized by relatively diverse and dynamic microbial community that is essential for maintaining ocular health and can be leveraged to enhance resistance against infectious ocular diseases. In this narrative review, we provide comprehensive insights into the ocular microbiota by summarizing the amplicon and metagenomic sequencing- and culture-based studies conducted in cattle, and by reviewing relevant findings from humans and other animal species. We also explore the potential of the ocular microbiome as a new frontier in managing IBK. Finally, we examine the gut-eye-microbiome axis and discuss its potential contribution in improving the resistance of cattle against IBK.

Farmed mink (Neovison vison) is the most common animal species used for fur farming in China. Several viruses identified in mink can be transmitted to humans, including SARS-CoV-2, suggesting that this species could play an important role in zoonotic disease emergence. Characterizing the virus diversity of farmed mink is therefore important for the prevention and mitigation of emerging infectious diseases. We utilized meta-transcriptomic sequencing to determine the enteric viromes of 109 apparently healthy farmed mink from Shandong and Liaoning provinces, China. Using this approach, we identified 34 viruses belonging to 11 viral families/clades. Several important avian- or fish-associated viruses were detected, including astroviruses, caliciviruses, picornaviruses, rotaviruses, parvoviruses, and gyroviruses. Many of these viruses were likely associated with mink diet, indicating that food sources such as uncooked poultry or fish by-products can serve as effective transmission routes of avian and fish viruses to mink. Of particular note, we identified a high prevalence of mink coronavirus in these animals, which is potentially associated with respiratory and gastrointestinal illnesses. In sum, our study revealed a diverse range of vertebrate viruses in farmed mink and likely viral transmission to mink via the food chain. Further investigation is necessary to determine the impact of these viruses on mink health and for zoonotic disease preparedness.

Caves are a challenging environment for many organisms to inhabit, and many cave-dwelling animals are endemic to particular cave systems. Microorganisms in caves have been shown to have a high biosynthetic capacity, likely as a result of intense biological interactions to deal with resource scarcity. Although cave salamanders have been studied extensively in other parts of the world, they have received relatively little attention in Mexico. Declines of some cave-dwelling species may be due to outbreaks of fungal disease, and a better understanding of their cutaneous microbiome could help with future conservation efforts in the face of disease outbreaks. We characterized the cutaneous microbiome of 11 cave-dwelling Mexican salamanders and their relatives from surface environments using high-throughput 16S amplicon sequencing. We expected cave salamanders to have a more diverse microbiome containing more bacteria with potential antifungal capacity compared to forest salamanders. We also estimated networks of associations between bacteria to test the hypothesis that there are more positive associations in caves. Finally, we used a bioinformatic approach to see if bacteria in caves potentially have more metabolic pathways associated with microbial communication as a result of more intense biological interactions in caves. Although we do not find higher skin bacterial diversity in caves compared to forests, we do find differences in microbiome composition between environments, more positive associations between bacteria, and a slightly higher number of metabolic pathways associated with microbial communication in caves. Our results provide some support for an impact of the cave environment on the skin microbiome of Mexican salamanders.