Yeasts of Burden: Exploring the Mycobiome-Bacteriome of the Piglet GI Tract

Potential of Non-Saccharomyces Yeasts as Probiotics and Alternatives to Antibiotics in Animal Production

Probiotics are live yeast or bacterial organisms that have beneficial effects on the host. Several microorganisms exhibit probiotic properties, the most common types being lactic acid bacteria, Bifidobacteria, spore-forming bacteria, and some yeast strains. Saccharomyces cerevisiae var. boulardii is the most important probiotic yeast species. However, another group of foodborne microorganisms, the so-called non-Saccharomyces yeasts (NSYs), has recently been re-evaluated and shown to have enormous potential in various fields of application, ranging from food fermentation to human and animal applications. NSYs are able to produce a range of bioactive compounds such as antimicrobials, mannoproteins, enzymes, polyunsaturated fatty acids, essential amino acids, vitamins, and β-glucans, which increases their potential applications as a new class of probiotics and/or alternatives to antibiotics in animal husbandry. In this review, we aim to highlight the potential and benefits of NSYs as probiotics and natural antimicrobials to improve animal health. Furthermore, the use of NSYs as biological alternatives to antibiotics to control foodborne pathogens in animal production is discussed.

Insights into gut fungi in pigs: A comprehensive review

Fungi in the gut microbiota of mammals play a crucial role in host physiological regulation, including intestinal homeostasis and host immune regulation. However, our understanding of gut fungi in mammals remains limited, especially in economically valuable animals, such as pigs. Therefore, this review first describes the classification and characterisation of fungi, provides insights into the methods used to study gut fungi, and summarises the recent progress on pig gut fungi. Additionally, it discusses the challenges in the study of pig gut fungi and highlights potential perspectives. The aim of this review is to serve as a valuable reference for advancing our knowledge of gut fungi in animals.

Weaning transition, but not the administration of probiotic candidate Kazachstania slooffiae, shaped the gastrointestinal bacterial and fungal communities in nursery piglets

As in-feed antibiotics are phased out of swine production, producers are seeking alternatives to facilitate improvements in growth typically seen from this previously common feed additive. Kazachstania slooffiae is a prominent commensal fungus in the swine gut that peaks in relative abundance shortly after weaning and has beneficial interactions with other bacteriome members important for piglet health. In this study, piglets were supplemented with K. slooffiae to characterize responses in piglet health as well as fungal and bacterial components of the microbiome both spatially (along the entire gastrointestinal tract and feces) and temporally (before, during, and after weaning). Litters were assigned to one of four treatments: no K. slooffiae (CONT); one dose of K. slooffiae 7 days before weaning (day 14; PRE); one dose of K. slooffiae at weaning (day 21; POST); or one dose of K. slooffiae 7 days before weaning and one dose at weaning (PREPOST). The bacteriome and mycobiome were analyzed from fecal samples collected from all piglets at day 14, day 21, and day 49, and from organ samples along the gastrointestinal (GI) tract at day 21 and day 49. Blood samples were taken at day 14 and day 49 for cytokine analysis, and fecal samples were assayed for antimicrobial resistance. While some regional shifts were seen in response to K. slooffiae administration in the mycobiome of the GI tract, no remarkable changes in weight gain or health of the animals were observed, and changes were more likely due to sow and the environment. Ultimately, the combined microbiome changed most considerably following the transition from suckling to nursery diets. This work describes the mycobiome along the piglet GI tract through the weaning transition for the first time. Based on these findings, K. slooffiae administered at this concentration may not be an effective tool to hasten colonization of K. slooffiae in the piglet GI tract around the weaning transition nor support piglet growth, microbial gut health, or immunity. However, diet and environment greatly influence microbial community development.

Tracking the fecal mycobiome through the lifespan of production pigs and a comparison to the feral pig

IMPORTANCE

This work provides evidence that early-life fungal community composition, or host genetics, influences long-term mycobiome composition. In addition, this work provides the first comparison of the feral pig mycobiome to the mycobiome of intensively raised pigs.

Draft Genome Sequence of a Primate Isolate of Kazachstania pintolopesii

Kazachstania pintolopesii is an opportunistic mammalian pathobiont from the K. telluris species complex. No draft genomes of this species are currently available. Here, we report the first draft genome sequence of a primate isolate of K. pintolopesii (NCYC 4417).

Combined effects of host genetics and diet on porcine intestinal fungi and their pathogenic genes

As research on gut microbes progresses, it becomes increasingly clear that a small family of microbiota--fungi, plays a crucial role in animal health. However, little is known about the fungal composition in the pig intestine, especially after a dietary fiber diet and hybrid genetics, and the changes in host pathogenicity-associated genes they carry. The purpose of this study is to investigate the effects of diet and genetics on the diversity and structure of porcine intestinal fungi and to describe, for the first time, the host pathogenicity-related genes carried by porcine intestinal fungi. Samples of colonic contents were collected for metagenomic analysis using a 3 × 2 parsing design, where three pig breeds (Taoyuan, Duroc, and crossbred Xiangcun) were fed high or low fiber diets (n = 10). In all samples, we identified a total of 281 identifiable fungal genera, with Ascomycota and Microsporidia being the most abundant fungi. Compared to Duroc pigs, Taoyuan and Xiangcun pigs had higher fungal richness. Interestingly, the fiber diet significantly reduced the abundance of the pathogenic fungus Mucor and significantly increased the abundance of the fiber digestion-associated fungus Neocallimastix. Pathogenic fungi exert their pathogenicity through the genes they carry that are associated with host pathogenicity. Therefore, we obtained 839 pathogenicity genes carried by the spectrum of fungi in the pig intestine by comparing the PHI-base database. Our results showed that fungi in the colon of Taoyuan pigs carried the highest abundance of different classes of host pathogenicity-related genes, and the lowest in Duroc pigs. Specifically, Taoyuan pigs carried high abundance of animal pathogenicity-related genes (CaTUP1, CPAR2_106400, CaCDC35, Tfp1, CaMNT2), and CaTUP1 was the key gene for Candida pathogenicity. The intestinal fungal composition of crossbred Xiangcun pigs and the abundance of host pathogenicity-associated genes they carried exhibited a mixture of characteristics of Taoyuan and Duroc pigs. In conclusion, our results provide the first comprehensive report on the effects of dietary fiber and genetics on the composition of intestinal fungi and the host-associated pathogenicity genes they carry in pigs. These findings provide a reference for subsequent pig breeding and development of anti-pathogenic fungal drugs.

Salmonella enterica induces biogeography-specific changes in the gut microbiome of pigs

Swine are a major reservoir of an array of zoonotic Salmonella enterica subsp. enterica lineage I serovars including Derby, Typhimurium, and 4,[5],12:i:- (a.k.a. Monophasic Typhimurium). In this study, we assessed the gastrointestinal (GI) microbiome composition of pigs in different intestinal compartments and the feces following infection with specific zoonotic serovars of S. enterica (S. Derby, S. Monophasic, and S. Typhimurium). 16S rRNA based microbiome analysis was performed to assess for GI microbiome changes in terms of diversity (alpha and beta), community structure and volatility, and specific taxa alterations across GI biogeography (small and large intestine, feces) and days post-infection (DPI) 2, 4, and 28; these results were compared to disease phenotypes measured as histopathological changes. As previously reported, only S. Monophasic and S. Typhimurium induced morphological alterations that marked an inflammatory milieu restricted to the large intestine in this experimental model. S. Typhimurium alone induced significant changes at the alpha- (Simpson's and Shannon's indexes) and beta-diversity levels, specifically at the peak of inflammation in the large intestine and feces. Increased community dispersion and volatility in colonic apex and fecal microbiomes were also noted for S. Typhimurium. All three Salmonella serovars altered community structure as measured by co-occurrence networks; this was most prominent at DPI 2 and 4 in colonic apex samples. At the genus taxonomic level, a diverse array of putative short-chain fatty acid (SCFA) producing bacteria were altered and often decreased during the peak of inflammation at DPI 2 and 4 within colonic apex and fecal samples. Among all putative SCFA producing bacteria, Prevotella showed a broad pattern of negative correlation with disease scores at the peak of inflammation. In addition, Prevotella 9 was found to be significantly reduced in all Salmonella infected groups compared to the control at DPI 4 in the colonic apex. In conclusion, this work further elucidates that distinct swine-related zoonotic serovars of S. enterica can induce both shared (high resilience) and unique (altered resistance) alterations in gut microbiome biogeography, which helps inform future investigations of dietary modifications aimed at increasing colonization resistance against Salmonella through GI microbiome alterations.

Characterization of the eukaryotic microbial communities in the chicken ileum in cage-free and conventional commercial housing systems

The current shift from conventional cage (CC) hen housing facilities towards cage-free (CF) hen housing in the egg industry has left many questions regarding how level of fecal exposure and exposure to other hens may influence the hen intestinal microbiota. In a previous publication we reported differences in the bacterial ileal communities and ileal morphology between hens in CC and CF production environments at a single commercial site. Here, we present the first 18S rRNA gene amplicon sequencing-based characterization of the eukaryotic ileal microbiota of adult layer hens, and their associations with intestinal health parameters and the bacterial microbiota. DNA was extracted from the ileal digesta of hens (n = 32 CC, n = 48 CF) using the Qiagen Powerlyzer Powersoil kit, followed by amplification of the V9 region of the 18S rRNA gene. Paired end sequencing was performed with the Illumina MiSeq platform, and the resulting reads were processed according to the Mothur MiSeq protocol in Mothur v1.43.0. De novo operational taxonomic unit (OTU) clustering was performed in mothur with a 99% similarity threshold, and OTUs were taxonomically classified with the SILVA SSU v138 reference database. OTUs classified as vertebrate, plant, or arthropod were removed, resulting in 3,136,400 high quality reads and 1,370 OTUs. Associations between OTUs and intestinal parameters were calculated using PROC GLIMMIX. PERMANOVA over Bray-Curtis distances revealed differences between CC and CF eukaryotic ileal microbiota at the whole community level, but no OTUs were differentially abundant after correcting for false discovery (P > 0.05; q > 0.1). Kazachstania and Saccharomyces, closely related genera of yeast, represented 77.1% and 9.7% of sequences respectively. Two Kazachstania OTUs and 1 Saccharomycetaceae OTU were positively correlated with intestinal permeability (r² ≥ 0.35). Eimeria accounted for 7.6% of sequences across all samples. Intriguingly, 15 OTUs classified as Eimeria were inversely associated with intestinal permeability (r² ≤ -0.35), suggesting Eimeria may play a more complex role in the microbiota of healthy birds than has been observed in disease challenges.

Core-predominant gut fungus Kazachstania slooffiae promotes intestinal epithelial glycolysis via lysine desuccinylation in pigs

BACKGROUND

Gut fungi are increasingly recognized as important contributors to host physiology, although most studies have focused on gut bacteria. Post-translational modifications (PTMs) of proteins play vital roles in cell metabolism. However, the contribution of gut fungi to host protein PTMs remains unclear. Mining gut fungi that mediate host protein PTMs and dissecting their mechanism are urgently needed.

RESULTS

We studied the gut fungal communities of 56 weaned piglets and 56 finishing pigs from seven pig breeds using internal transcribed spacer (ITS) gene amplicon sequencing and metagenomics. The results showed that Kazachstania slooffiae was the most abundant gut fungal species in the seven breeds of weaned piglets. K. slooffiae decreased intestinal epithelial lysine succinylation levels, and these proteins were especially enriched in the glycolysis pathway. We demonstrated that K. slooffiae promoted intestinal epithelial glycolysis by decreasing lysine succinylation by activating sirtuin 5 (SIRT5). Furthermore, K. slooffiae-derived 5'-methylthioadenosine metabolite promoted the SIRT5 activity.

CONCLUSIONS

These findings provide a landscape of gut fungal communities of pigs and suggest that K. slooffiae plays a crucial role in intestinal glycolysis metabolism through lysine desuccinylation. Our data also suggest a potential protective strategy for pigs with an insufficient intestinal energy supply. Video Abstract.

Description of Gut Mycobiota Composition and Diversity of Caprinae Animals

The fungal community, also known as mycobiota, plays pivotal roles in host nutrition and metabolism and has potential to cause disease. However, knowledge of the gut fungal structure in Caprinae is quite limited. In this study, the composition and diversity of the gut mycobiota of Caprinae animals from different geographical locations (Anhui, Jilin, Guangxi, Shandong, Shanxi, and Tibet) were comprehensively characterized by analyzing the internal transcribed spacer 2 (ITS-2) sequences of the fungal community. The results showed that Ascomycota and Basidiomycota were the dominant phyla, which, respectively, accounted for 90.86 to 95.27% and 2.58 to 7.62% of sequences in samples from each region. Nonetheless, the structure of the gut mycobiota was largely different in Caprinae animals in the different provinces. Therein, Sporormiaceae and Thelebolaceae were the dominant fungal families in the samples from Tibet, whereas their abundance was generally low in other regions. The intestinal diversity of individuals from Guangxi was higher than that in other regions. In addition, there were 114 differential genera among all regions. Finally, the co-occurrence network revealed 285 significant correlations in cross-family pairs in the guts of Caprinae animals, which contained 149 positive and 136 negative relationships, with 96 bacterial and 86 fungal participants at the family level. This study has improved the understanding of the mycobiota of ruminants and provided support for the improvement in animal health and productivity. IMPORTANCE In this study, we elucidated and analyzed the structure of the gut mycobiota of Caprinae animals from different regions. This study revealed differences in the structure of the gut mycobiota among Caprinae animals from different geographical environments. Based on previous findings, correlations between fungal and bacterial communities were analyzed. This study adds to previous research that has expanded the present understanding of the gut microbiome of Caprinae animals.

Porcine fungal mock community analyses: Implications for mycobiome investigations

Introduction

The gut microbiome is an integral partner in host health and plays a role in immune development, altered nutrition, and pathogen prevention. The mycobiome (fungal microbiome) is considered part of the rare biosphere but is still a critical component in health. Next generation sequencing has improved our understanding of fungi in the gut, but methodological challenges remain. Biases are introduced during DNA isolation, primer design and choice, polymerase selection, sequencing platform selection, and data analyses, as fungal reference databases are often incomplete or contain erroneous sequences.

Methods

Here, we compared the accuracy of taxonomic identifications and abundances from mycobiome analyses which vary among three commonly selected target gene regions (18S, ITS1, or ITS2) and the reference database (UNITE - ITS1, ITS2 and SILVA - 18S). We analyze multiple communities including individual fungal isolates, a mixed mock community created from five common fungal isolates found in weanling piglet feces, a purchased commercial fungal mock community, and piglet fecal samples. In addition, we calculated gene copy numbers for the 18S, ITS1, and ITS2 regions of each of the five isolates from the piglet fecal mock community to determine whether copy number affects abundance estimates. Finally, we determined the abundance of taxa from several iterations of our in-house fecal community to assess the effects of community composition on taxon abundance.

Results

Overall, no marker-database combination consistently outperformed the others. Internal transcribed space markers were slightly superior to 18S in the identification of species in tested communities, but Lichtheimia corymbifera, a common member of piglet gut communities, was not amplified by ITS1 and ITS2 primers. Thus, ITS based abundance estimates of taxa in piglet mock communities were skewed while 18S marker profiles were more accurate. Kazachstania slooffiae displayed the most stable copy numbers (83-85) while L. corymbifera displayed significant variability (90-144) across gene regions.

Discussion

This study underscores the importance of preliminary studies to assess primer combinations and database choice for the mycobiome sample of interest and raises questions regarding the validity of fungal abundance estimates.

Fungal-Bacterial Interactions in the Human Gut of Healthy Individuals

Most studies of the microbiota in the human gut focus on the bacterial part, but increasing information shows that intestinal fungi are also important for maintaining health. This can be either by directly influencing the host or by indirectly influencing the gut bacteria that link to host health. Studies of fungal communities in large cohorts are scarce; therefore, this study aims at obtaining more insight into the mycobiome of healthy individuals and how this mycobiome interacts with the bacterial component of the microbiome. For this purpose, ITS2 and 16S rRNA gene amplicon sequencing was performed on fecal samples from 163 individuals which were available from two separate studies to analyze the fungal and bacterial microbiome, respectively, as well as the cross-kingdom interactions. The results showed a much lower fungal, as compared to bacterial, diversity. Ascomycota and Basidiomycota were the dominant fungal phyla across all the samples, but levels varied enormously between individuals. The ten most abundant fungal genera were Saccharomyces, Candida, Dipodascus, Aureobasidium, Penicillium, Hanseniaspora, Agaricus, Debaryomyces, Aspergillus, and Pichia, and here also extensive inter-individual variation was observed. Correlations were made between bacteria and fungi, and only positive correlations were observed. One of the correlations was between Malassezia restricta and the genus Bacteroides, which have both been previously described as alleviated in IBD. Most of the other correlations found were with fungi that are not known as gut colonizers but originate from food and the environment. To further investigate the importance of the observed correlations found, more research is needed to discriminate between gut colonizers and transient species.

Maternal Mycobiome, but Not Antibiotics, Alters Fungal Community Structure in Neonatal Piglets

Early-life antibiotic exposure is associated with diverse long-term adverse health outcomes. Despite the immunomodulatory effects of gastrointestinal fungi, the impact of antibiotics on the fungal community (mycobiome) has received little attention. The objectives of this study were to determine the impact of commonly prescribed infant antibiotic treatments on the microbial loads and structures of bacterial and fungal communities in the gastrointestinal tract. Thirty-two piglets were divided into four treatment groups: amoxicillin (A), amoxicillin-clavulanic acid (AC), gentamicin-ampicillin (GA), and flavored placebo (P). Antibiotics were administered orally starting on postnatal day (PND) 1 until PND 8, except for GA, which was given on PNDs 5 and 6 intramuscularly. Fecal swabs were collected from piglets on PNDs 3 and 8, and sow feces were collected 1 day after farrowing. The impacts of antibiotics on bacterial and fungal communities were assessed by sequencing the 16S rRNA and the internal transcribed spacer 2 (ITS2) rRNA genes, respectively, and quantitative PCR was performed to determine total bacterial and fungal loads. Antibiotics did not alter the α-diversity (P = 0.834) or β-diversity (P = 0.565) of fungal communities on PND 8. AC increased the ratio of total fungal/total bacterial loads on PND 8 (P = 0.027). There was strong clustering of piglets by litter on PND 8 (P < 0.001), which corresponded to significant differences in the sow mycobiome, especially the presence of Kazachstania slooffiae. In summary, we observed a strong litter effect and showed that the maternal mycobiome is essential for shaping the piglet mycobiome in early life. IMPORTANCE This work provides evidence that although the fungal community composition is not altered by antibiotics, the overall fungal load increases with the administration of amoxicillin-clavulanic acid. Additionally, we show that the maternal fungal community is important in establishing the fungal community in piglets.

Batch and sampling time exert a larger influence on the fungal community than gastrointestinal location in model animals: A meaningful case study

Fungi play a fundamental role in the intestinal ecosystem and health, but our knowledge of fungal composition and distribution in the whole gastrointestinal tract (GIT) is very limited. The physiological similarity between humans and pigs in terms of digestive and associated metabolic processes places, the pig in a superior position over other non-primate models. Here, we aimed to characterize the diversity and composition of fungi in the GIT of pigs. Using high-throughput sequencing, we evaluated the fungal community in different locations of GIT of 11 pigs with 128.41 ± 1.25 kg body weight acquired successively. Among them, five pigs are sacrificed in April 2019 (Batch 1) and the other six are sacrificed in January 2020 (Batch 2). All subjects with similar genetic backgrounds, housing, management, and diet. Finally, no significant difference is found in the α-diversity (Richness) of the fungal community among all intestinal segments. Basidiomycota and Ascomycota are the two predominant fungal phyla, but Batch 1 harbored a notably high abundance of Basidiomycota and Batch 2 harbored a high abundance of Ascomycota. Moreover, the two batches harbored completely different fungal compositions and core fungal genera. FUNGuild (Fungal Functional Guild) analysis revealed that most of the fungal species present in the GIT are saprotroph, plant pathogen, and animal endosymbiont. Our study is the first to report that even under the same condition, large variations in fungal composition in the host GIT still occur from batch-to-batch and sampling time. The implications of our observations serve as references to the development of better models of the human gut.

The Cynomolgus Macaque Intestinal Mycobiome Is Dominated by the Kazachstania Genus and K. pintolopesii Species

The cynomolgus macaque, Macaca fascicularis, is a non-human primate (NHP) widely used in biomedical research as its genetics, immunology and physiology are similar to those of humans. They may also be a useful model of the intestinal microbiome as their prokaryome resembles that of humans. However, beyond the prokaryome relatively little is known about other constituents of the macaque intestinal microbiome including the mycobiome. Here, we conducted a region-by-region taxonomic survey of the cynomolgus intestinal mycobiota, from duodenum to distal colon, of sixteen captive animals of differing age (from young to old). Using a high-throughput ITS1 amplicon sequencing-based approach, the cynomolgus gut mycobiome was dominated by fungi from the Ascomycota phylum. The budding yeast genus Kazachstania was most abundant, with the thermotolerant species K. pintolopesii highly prevalent, and the predominant species in both the small and large intestines. This is in marked contrast to humans, in which the intestinal mycobiota is characterised by other fungal genera including Candida and Saccharomyces, and Candida albicans. This study provides a comprehensive insight into the fungal communities present within the captive cynomolgus gut, and for the first time identifies K. pintolopesii as a candidate primate gut commensal.

Stability and volatility shape the gut bacteriome and Kazachstania slooffiae dynamics in preweaning, nursery and adult pigs

The gut microbiome plays important roles in the maintenance of health and pathogenesis of diseases in the growing host. In order to fully comprehend the interplay of the gut microbiome and host, a foundational understanding of longitudinal microbiome, including bacteria and fungi, development is necessary. In this study, we evaluated enteric microbiome and host dynamics throughout the lifetime of commercial swine. We collected a total of 234 fecal samples from ten pigs across 31 time points in three developmental stages (5 preweaning, 15 nursery, and 11 growth adult). We then performed 16S rRNA gene amplicon sequencing for bacterial profiles and qPCR for the fungus Kazachstania slooffiae. We identified distinct bacteriome clustering according to the host developmental stage, with the preweaning stage exhibiting low bacterial diversity and high volatility amongst samples. We further identified clusters of bacteria that were considered core, increasing, decreasing or stage-associated throughout the host lifetime. Kazachstania slooffiae was absent in the preweaning stage but peaked during the nursery stage of the host. We determined that all host growth stages contained negative correlations between K. slooffiae and bacterial genera, with only the growth adult stage containing positive correlates. Our stage-associated bacteriome results suggested the neonate contained a volatile gut microbiome. Upon weaning, the microbiome became relatively established with comparatively fewer perturbations in microbiome composition. Differential analysis indicated bacteria might play distinct stage-associated roles in metabolism and pathogenesis. The lack of positive correlates and shared K. slooffiae-bacteria interactions between stages warranted future research into the interactions amongst these kingdoms for host health. This research is foundational for understanding how bacteria and fungi develop singularly, as well as within a complex ecosystem in the host's gut environment.

Gut archaea associated with bacteria colonization and succession during piglet weaning transitions

Background

Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods.

Results

We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3.

Conclusion

Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03330-4.

Drinking Water Supplemented with Acidifiers Improves the Growth Performance of Weaned Pigs and Potentially Regulates Antioxidant Capacity, Immunity, and Gastrointestinal Microbiota Diversity

This study evaluated the potential effects of adding acidifiers to the drinking water on the growth performance, complete blood count, antioxidant indicators, and diversity of gastrointestinal microbiota for weaned pigs. A total of 400 weaned pigs were randomly divided into four treatments. Pigs were fed the same basal diet and given either water (no acidifier was added, control) or water plus blends of different formulas of acidifiers (acidifier A1, A2, or A3) for 35 days. On d 18 and 35 of the experimental period, 64 pigs (four pigs per pen) were randomly selected to collect blood for a CBC test (n = 128) and an antioxidant indicators test (n = 128); 24 pigs (six pigs per group) were randomly selected to collect fresh feces (n = 48) from the rectum for 16S rRNA gene sequencing. Compared to the control, supplementing the drinking water with acidifiers improved the growth performance and survival rate of weaned pigs. Acidifier groups also increased serum catalase (CAT) and total antioxidant capacity (T-AOC) activities, while also displaying a decreased malondialdehyde (MDA) concentration compared to the control. The relative abundance of Firmicutes in the acidifier A1 group was greater than that in the control group (p < 0.05) on d 35; the relative abundance of Lactobacillus in the acidifier A1 group was greater than that in the control group (p < 0.05) on d 18 and 35. The microbial species Subdoligranulum or Ruminococcaceae_UCG-005 had significantly positive correlations with ADG and ADFI or with serum antioxidant indicators, respectively. These findings suggest that supplementing the drinking water with an acidifier has a potential as an antioxidant, which was reflected in the improvement of growth performance, immunity, antioxidant capacity, and intestinal flora.

Biogeography, succession, and origin of the chicken intestinal mycobiome

BACKGROUND

Extensive work has been accomplished to characterize the intestinal bacterial community, known as the microbiota, and its association with host health and disease. However, very little is known about the spatiotemporal development and the origin of a minor intestinal fungal community, known as the mycobiota, in humans and animals, particularly in avian species.

RESULTS

In this study, we comprehensively characterized the biogeography and succession of the gastrointestinal (GI) mycobiota of broiler chickens and further revealed the fungal sources that are responsible for initial and long-term establishment of the mycobiota in the GI tract. Using Illumina sequencing of the internal transcribed spacer 2 (ITS2) region of fungal rRNA genes, we detected significant spatial and temporal differences in the mycobiota along the GI tract. In contrary to the microbiota, the mycobiota was more diverse in the upper than the lower GI tract with no apparent trend of succession up to 42 days of age. The intestinal mycobiota was dominated by the phyla Ascomycota and Basidiomycota with Gibberella, Aspergillus, and Candida being the most abundant genera. Although the chicken mycobiota was highly dynamic, Fusarium pseudonygamai was dominant throughout the GI tract regardless of age in this study. The core chicken mycobiome consisted of 26 fungal taxa accounting for greater than 85% of the fungal population in each GI location. However, we observed high variations of the intestinal mycobiota among different studies. We also showed that the total fungal population varied greatly from 1.0 × 10⁴ to 1.1 × 10⁶ /g digesta along the GI tract and only accounted for less than 0.06% of the bacteria in day-42 broilers. Finally, we revealed that the mycobiota from the hatchery environment was responsible for initial colonization in the GI tract of newly hatched chickens, but was quickly replaced by the fungi in the diet within 3 days.

CONCLUSIONS

Relative to the intestinal microbiota that consists of trillions of bacteria in hundreds of different species and becomes relatively stabilized as animals age, the chicken intestinal mycobiota is a minor microbial community that is temporally dynamic with limited diversity and no obvious pattern of successive changes. However, similar to the microbiota, the chicken mycobiota is spatially different along the GI tract, although it is more diverse in the upper than the lower GI tract. Dietary fungi are the major source of the intestinal mycobiota in growing chickens. Video abstract.

Microbial Quality of Liquid Feed for Pigs and Its Impact on the Porcine Gut Microbiome

Simple Summary

Liquid feed is produced by mixing dry feed ingredients with water, and sometimes liquid co-products from the food and beverage industry, at a defined ratio. Liquid feeding of pigs is popular, particularly in parts of northern and western Europe, and can be associated with lower feed costs, improved dry matter intake, growth rate and gut health, compared to dry feeding. However, spontaneous/uncontrolled fermentation upon mixing of feed with water or co-products can decrease the microbial and nutritional quality of the feed, resulting in poorer pig health and growth. For this reason, strategies aimed at optimising liquid feed microbial quality are frequently employed. These include: deliberate fermentation with/without the use of lactic acid bacteria starter cultures that produce lactic acid and lower the feed pH, thereby preventing growth of pathogens. Fermenting only the cereal component of the diet is preferred to whole diet fermentation to minimise loss of free amino acids from the diet during fermentation. This review examines the microbiome of liquid feed and explores how optimisation strategies impact both feed microbial quality and the gut microbiota and growth of liquid-fed pigs. It also covers cleaning and disinfection of liquid feeding systems and how this might impact liquid feed microbial quality.

Abstract

There is evidence that spontaneous fermentation frequently occurs in liquid pig feed that is intended to be delivered as fresh liquid feed, often with a resultant deterioration in the microbial and nutritional quality of the feed, which can negatively affect pig health and growth. Strategies including controlled fermentation with microbial inoculants, pre-fermentation or soaking of the cereal fraction of the diet, enzyme supplementation and dietary acidification have been employed to inhibit pathogens and prevent deterioration of feed nutritional quality, with promising results obtained in many cases. This review evaluates the impact of these strategies on the microbial quality of liquid feed and discusses how they can be further improved. It also investigates if/how these strategies impact the pig gut microbiota and growth performance of liquid-fed pigs. Finally, we review liquid feed system sanitisation practices, which are highly variable from farm to farm and discuss the impact of these practices and whether they are beneficial or detrimental to liquid feed microbial quality. Overall, we provide a comprehensive review of the current state of knowledge on liquid feed for pigs, focusing on factors affecting microbial quality and strategies for its optimisation, as well as its impact on the pig gut microbiome.

The role of gut mycobiome in health and diseases

The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut "mycobiome") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.

Draft Genome Sequence of Kazachstania slooffiae, Isolated from Postweaning Piglet Feces

Kazachstania slooffiae is a dimorphic fungus which colonizes the feces and gastrointestinal tract of postweaning pigs. This fungus persists in the gut environment of piglets into adulthood and is implicated in porcine health through microbe-microbe and microbe-host interactions. Here, we report a draft genome sequence for K. slooffiae ABBL.

Characterization of Kazachstania slooffiae, a Proposed Commensal in the Porcine Gut

Kazachstania slooffiae is a fungus commonly isolated from the gastrointestinal tract and feces of post-weaning pigs. Studies have implicated its ability to positively alter piglet gut health through potential symbioses with beneficial bacteria, including Lactobacillus and Prevotella, in providing amino acids as an energy source for microbial and piglet growth, and it has been found to be positively correlated with short-chain fatty acids in the piglet gut. However, basic mycological information remains limited, hampering in vitro studies. In this study, we characterized the growth parameters, biofilm formation ability, susceptibility to antimicrobials, and genetic relatedness of K. slooffiae to other fungal isolates. Optimal fungal growth conditions were determined, no antifungal resistance was found against multiple classes of antifungal drugs (azoles, echinocandins, polyenes, or pyrimidine analogues), and dimorphic growth was observed. K. slooffiae produced biofilms that became more complex in the presence of Lactobacillus acidophilus supernatant, suggesting positive interactions with this bacterium in the gut, while Enterococcus faecalis supernatant decreased density, suggesting an antagonistic interaction. This study characterizes the in vitro growth conditions that are optimal for further studies of K. slooffiae, which is an important step in defining the role and interactions of K. slooffiae in the porcine gut environment.

A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.

The authors present a public collection of 117 bacterial isolates from the pig gut, including the description of 38 novel taxa. Interesting functions discovered in these organisms include a new fucosyltransferease and sactipeptide-like molecules encoded by biosynthetic gene clusters.

Fungal Dysbiosis Correlates with the Development of Tumor-Induced Cachexia in Mice

Cachexia (CC) is a devastating metabolic syndrome associated with a series of underlying diseases that greatly affects life quality and expectancy among cancer patients. Studies involving mouse models, in which CC was induced through inoculation with tumor cells, originally suggested the existence of a direct correlation between the development of this syndrome and changes in the relative proportions of several bacterial groups present in the digestive tract. However, these analyses have focus solely on the characterization of bacterial dysbiosis, ignoring the possible existence of changes in the relative populations of fungi, during the development of CC. Thus, the present study sought to expand such analyses, by characterizing changes that occur in the gut fungal population (mycobiota) of mice, during the development of cancer-induced cachexia. Our results confirm that cachectic animals, submitted to Lewis lung carcinoma (LLC) transplantation, display significant differences in their gut mycobiota, when compared to healthy controls. Moreover, identification of dysbiotic fungi showed remarkable consistency across successive levels of taxonomic hierarchy. Many of these fungi have also been associated with dysbioses observed in a series of gut inflammatory diseases, such as obesity, colorectal cancer (CRC), myalgic encephalomyelitis (ME) and inflammatory bowel disease (IBD). Nonetheless, the dysbiosis verified in the LLC model of cancer cachexia seems to be unique, presenting features observed in both obesity (reduced proportion of Mucoromycota) and CRC/ME/IBD (increased proportions of Sordariomycetes, Saccharomycetaceae and Malassezia). One species of Mucoromycota (Rhyzopus oryzae) stands out as a promising probiotic candidate in adjuvant therapies, aimed at treating and/or preventing the development of CC.

Oral-fecal mycobiome in wild and captive cynomolgus macaques (Macaca fascicularis)

Cynomolgus macaque (Macaca fascicularis) is currently a common animal model for biomedical research. The National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU) translocated wild-borne macaques to reared colony for research purposes. At present, no studies focus on fungal microbiome (Mycobiome) of this macaque. The functional roles of mycobiome and fungal pathogens have not been elucidated. Thus, this study aimed to investigate and compare oral and fecal mycobiome between wild and captive macaques by using high-throughput sequencing on internal transcribed spacer 2 (ITS2) rDNA. The results showed that the mycobiome of wild macaque has greater alpha diversity. The fecal mycobiome has more limited alpha diversity than those in oral cavity. The community is mainly dominated by saprophytic yeast in Kasachstania genus which is related to aiding metabolic function in gut. The oral microbiome of most captive macaques presented the Cutaneotrichosporon suggesting the fungal transmission through skin-oral contact within the colony. The potential pathogens that would cause harmful transmission in reared colonies were not found in either group of macaques but the pathogen prevention and animal care is still important to be concerned. In conclusion, the results of gut mycobiome analysis in Thai cynomolgus macaques provide us with the basic information of oral and fecal fungi and for monitoring macaque's health status for animal care of research use.

Influence of the Fermented Feed and Vaccination and Their Interaction on Parameters of Large White/Norwegian Landrace Piglets

The aim of this study was to evaluate the influence of fermented with a newly isolated lactic acid bacteria (LAB) strains combination (Lactobacillus plantarum LUHS122, Lactobacillus casei LUHS210, Lactobacillus farraginis LUHS206, Pediococcus acidilactici LUHS29, Lactobacillus plantarum LUHS135 and Lactobacillus uvarum LUHS245) feed on non-vaccinated (NV) and vaccinated with Circovac porcine circovirus type 2 vaccine (QI09AA07, CEVA-PHYLAXIA Co. Ltd. Szállás u. 5. 1107 Budapest, Hungary) piglets' blood parameters, gut microbial composition, growth performance and ammonia emission. The 36-day experiment was conducted using 25-day-old Large White/Norwegian Landrace (LW/NL) piglets, which were randomly divided into four groups with 100 piglets each: S_nonV-non-vaccinated piglets fed with control group compound feed; S_V-vaccinated piglets fed with control group compound feed; RF_nonV-non-vaccinated piglets fed with fermented compound feed; RF_V-vaccinated piglets fed with fermented compound feed. Samples from 10 animals per group were collected at the beginning and end of the experiment. Metagenomic analysis showed that fermentation had a positive impact on the Lactobacillus prevalence during the post-weaning period of pigs, and vaccination had no negative impact on microbial communities. Although a higher amount of Lactobacillus was detected in vaccinated, compared with non-vaccinated groups. At the end of experiment, there was a significantly higher LAB count in the faeces of both vaccinated compared to non-vaccinated groups (26.6% for S_V and 17.2% for RF_V), with the highest LAB count in the S_V group. At the end of experiment, the S_V faeces also had the highest total bacteria count (TBC). The RF_V group had a 13.2% increase in total enterobacteria count (TEC) at the end of experiment, and the S_V group showed a 31.2% higher yeast/mould (Y/M) count. There were no significant differences in the average daily gain (ADG) among the groups; however, there were significant differences in the feed conversion ratios (FCR) between several groups: S_V vs. S_nonV (11.5% lower in the S_V group), RF_V vs. RF_nonV (10.2% lower in the RFnonV group) and S_V vs. RF_V (21.6% lower in the S_V group). Furthermore, there was a significant, very strong positive correlation between FCR and TEC in piglets' faeces (R = 0.919, p = 0.041). The lowest ammonia emission was in RF_V group section (58.2, 23.8, and 47.33% lower compared with the S_nonV, S_V and RF_nonV groups, respectively). Notably, there was lower ammonia emission in vaccinated groups (45.2% lower in S_V vs. S_nonV and 47.33% lower in RF_V vs. RF_nonV). There was also a significant, very strong positive correlation between ammonia emission and Y/M count in piglets' faeces at the end of the experiment (R = 0.974; p = 0.013). Vaccination as a separate factor did not significantly influence piglets' blood parameters. Overall, by changing from an extruded soya to cheaper rapeseed meal and applying the fermentation model with the selected LAB combination, it is possible to feed piglets without any undesirable changes in health and growth performance in a more sustainable manner. However, to evaluate the influence of vaccination and its interaction with other parameters (feed, piglets' age, breed, etc.) on piglets' parameters, additional studies should be performed and methods should be standardised to ensure the results may be compared.

Arntzen M, Ånestad R, Terrapon N, Gaby JC, Westereng B. Isolation and Characterization of Extracellular Vesicles Secreted In Vitro by Porcine Microbiota

The secretion of extracellular vesicles, EVs, is a common process in both prokaryotic and eukaryotic cells for intercellular communication, survival, and pathogenesis. Previous studies have illustrated the presence of EVs in supernatants from pure cultures of bacteria, including Gram-positive and Gram-negative glycan-degrading gut commensals. However, the isolation and characterization of EVs secreted by a complex microbial community have not been clearly reported. In a recent paper, we showed that wood-derived, complex β-mannan, which shares a structural similarity with conventional dietary fibers, can be used to modulate the porcine gut microbiota composition and activity. In this paper, we investigated the production, size, composition, and proteome of EVs secreted by pig fecal microbiota after 24 h enrichment on complex β-mannan. Using transmission electron microscopy and nanoparticle tracking analysis, we identified EVs with an average size of 165 nm. We utilized mass spectrometry-based metaproteomic profiling of EV proteins against a database of 355 metagenome-assembled genomes (MAGs) from the porcine colon and thereby identified 303 proteins. For EVs isolated from the culture grown on β-mannan, most proteins mapped to two MAGs, MAG53 and MAG272, belonging to the orders Clostridiales and Bacilli, respectively. Furthermore, the MAG with the third-most-detected protein was MAG 343, belonging to the order Enterobacteriales. The most abundant proteins detected in the β-mannan EVs proteome were involved in translation, energy production, amino acid, and carbohydrate transport, as well as metabolism. Overall, this proof-of-concept study demonstrates the successful isolation of EVs released from a complex microbial community; furthermore, the protein content of the EVs reflects the response of specific microbes to the available carbohydrate source.

Potential Respiratory Deposition and Species Composition of Airborne Culturable, Viable, and Non-Viable Fungi during Occupancy in a Pig Farm

Fungal species composition and site of deposition within the airways affects whether diseases develop and where they may arise. The aim of this study is to obtain knowledge regarding the potential deposition of airborne culturable, viable, and non-viable fungi in the airways of pig farm workers, and how this composition changes over multiple sampling days. Airborne fungi were sampled using impactors and subsequently analyzed using amplicon sequencing and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) fingerprinting. The geometric mean aerodynamic diameter (Dg) of airborne particles with culturable airborne fungi were not affected by sampling days and ranged in size between 3.7 and 4.6 µm. Amplicon sequencing of the internal transcribed spacer region of the rRNA gene operon, in combination with DNA interchelating agents, revealed a large presence of non-viable fungi, but several pathogenic and toxic fungal species were detected in the viable portion. The diversity was found to be significantly associated with the sampling day but did not change significantly over multiple sampling rounds during the same day. The non-viable fraction contained genera typically associated with the pig gastrointestinal tract, such as Kazachstania and Vishniacozyma. In conclusion, the Dg of culturable fungi was between 3.7 and 4.6 µm, and the Dg of the viable and total fungi was 1.5 and 2.1 µm, respectively. The species composition changed over the multiple sampling days.

Temporal Dynamics of the Gut Bacteriome and Mycobiome in the Weanling Pig

Weaning is a period of environmental changes and stress that results in significant alterations to the piglet gut microbiome and is associated with a predisposition to disease, making potential interventions of interest to the swine industry. In other animals, interactions between the bacteriome and mycobiome can result in altered nutrient absorption and susceptibility to disease, but these interactions remain poorly understood in pigs. Recently, we assessed the colonization dynamics of fungi and bacteria in the gastrointestinal tract of piglets at a single time point post-weaning (day 35) and inferred interactions were found between fungal and bacterial members of the porcine gut ecosystem. In this study, we performed a longitudinal assessment of the fecal bacteriome and mycobiome of piglets from birth through the weaning transition. Piglet feces in this study showed a dramatic shift over time in the bacterial and fungal communities, as well as an increase in network connectivity between the two kingdoms. The piglet fecal bacteriome showed a relatively stable and predictable pattern of development from Bacteroidaceae to Prevotellaceae, as seen in other studies, while the mycobiome demonstrated a loss in diversity over time with a post-weaning population dominated by Saccharomycetaceae. The mycobiome demonstrated a more transient community that is likely driven by factors such as diet or environmental exposure rather than an organized pattern of colonization and succession evidenced by fecal sample taxonomic clustering with nursey feed samples post-weaning. Due to the potential tractability of the community, the mycobiome may be a viable candidate for potential microbial interventions that will alter piglet health and growth during the weaning transition.

Gut eukaryotic communities in pigs: diversity, composition and host genetics contribution

BACKGROUND

The pig gut microbiome harbors thousands of species of archaea, bacteria, viruses and eukaryotes such as protists and fungi. However, since the majority of published studies have been focused on prokaryotes, little is known about the diversity, host-genetic control, and contributions to host performance of the gut eukaryotic counterparts. Here we report the first study that aims at characterizing the diversity and composition of gut commensal eukaryotes in pigs, exploring their putative control by host genetics, and analyzing their association with piglets body weight.

RESULTS

Fungi and protists from the faeces of 514 healthy Duroc pigs of two sexes and two different ages were characterized by 18S and ITS ribosomal RNA gene sequencing. The pig gut mycobiota was dominated by yeasts, with a high prevalence and abundance of Kazachstania spp. Regarding protists, representatives of four genera (Blastocystis, Neobalantidium, Tetratrichomonas and Trichomitus) were predominant in more than the 80% of the pigs. Heritabilities for the diversity and abundance of gut eukaryotic communities were estimated with the subset of 60d aged piglets (N = 390). The heritabilities of α-diversity and of the abundance of fungal and protists genera were low, ranging from 0.15 to 0.28. A genome wide association study reported genetic variants related to the fungal α-diversity and to the abundance of Blastocystis spp. Annotated candidate genes were mainly associated with immunity, gut homeostasis and metabolic processes. Additionally, we explored the association of gut commensal eukaryotes with piglet body weight. Our results pointed to a positive contribution of fungi from the Kazachstania genus, while protists displayed both positive (Blastocystis and Entamoeba) and negative (Trichomitus) associations with piglet body weight.

CONCLUSIONS

Our results point towards a minor and taxa specific genetic control over the diversity and composition of the pig gut eukaryotic communities. Moreover, we provide evidences of the associations between piglets' body weight after weaning and members from the gut fungal and protist eukaryote community. Overall, this study highlights the relevance of considering, along with that of bacteria, the contribution of the gut eukaryote communities to better understand host-microbiome association and their role on pig performance, welfare and health.