Gut microbiota plays fundamental roles in energy harvest, nutrient digestion, and intestinal health, especially in processing indigestible components of polysaccharides in diet. Unraveling the ...microbial taxa and functional capacity of gut microbiome associated with feed efficiency can provide important knowledge to improve pig feed efficiency in swine industry. In the current research, we studied the association of fecal microbiota with feed efficiency in 280 commercial Duroc pigs. All experimental pigs could be clustered into two enterotype-like groups. Different enterotypes showed the tendency of association with the feed efficiency (
= 0.07). We further identified 31 operational taxonomic units (OTUs) showing the potential associations with porcine feed efficiency. These OTUs were mainly annotated to the bacteria related to the metabolisms of dietary polysaccharides. Although we did not identify the RFI-associated bacterial species at FDR < 0.05 level, metagenomic sequencing analysis did find the distinct function capacities of gut microbiome between the high and low RFI pigs (FDR < 0.05). The KEGG orthologies related to nitrogen metabolism, amino acid metabolism, and transport system, and eight KEGG pathways including glycine, serine, and threonine metabolism were positively associated with porcine feed efficiency. We inferred that gut microbiota might improve porcine feed efficiency through promoting intestinal health by the SCFAs produced by fermenting dietary polysaccharides and improving the utilization of dietary protein. The present results provided important basic knowledge for improving porcine feed efficiency through modulating gut microbiome.
The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, ...e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs.
Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis.
The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota.
Pigs are a perfect model for studying the interaction between host genetics and gut microbiome due to the high similarity of gastrointestine and digestive system with humans, and the easily ...controlled feeding conditions. In this study, two pig populations which were raised in uniformed farm conditions and provided with the same commercial formula diet were used as the experimental animals. A systematical investigation of host genetic effect on the gut microbial composition was separately performed in porcine cecum lumen and feces samples through the comparison of microbial composition among full-sibs, half-sibs and unrelated members, heritability estimate (
), and genome-wide association study (GWAS). The results showed that full-sib members had a higher similarity of microbial composition than unrelated individuals. A significant correlation was observed between the microbial composition-based kinship and the host SNP-based kinship in both populations (
< 9.9 × 10
). We identified 81 and 67 microbial taxa having
> 0.15 in fecal and cecum luminal samples, respectively, including 31 taxa with
> 0.15 in both types of samples. GWAS identified 40 and 34 significant associations between host genomic loci and the abundance or presence/absence of bacterial taxa in the fecal and cecum luminal samples. Functional classifications of host candidate genes related to microbial taxa are mainly associated with metabolism, immunity functions and response, and signal transduction. The high similarity of heritable taxa and functional categories of candidate genes among pig, human and mouse suggests the similar mechanism of the host genetic effect on gut microbiome across mammalian species. The results from this study provided another evidence that host genetics contributes significantly to the gut microbiome.
There are growing evidences showing that gut microbiota should play an important role in host appetite and feeding behavior. However, what kind of microbe(s) and how they affect porcine appetite ...remain unknown.
In this study, 280 commercial Duroc pigs were raised in a testing station with the circadian feeding behavior records for a continuous period of 30-100 kg. We first analyzed the influences of host gender and genetics in porcine average daily feed intake (ADFI), but no significant effect was observed. We found that the Prevotella-predominant enterotype had a higher ADFI than the Treponema enterotype-like group. Furthermore, 12 out of the 18 OTUs positively associated with the ADFI were annotated to Prevotella, and Prevotella was the hub bacteria in the co-abundance network. These results suggested that Prevotella might be a keystone bacterial taxon for increasing host feed intake. However, some bacteria producing short-chain fatty acids (SCFAs) and lactic acid (e.g. Ruminococcaceae and Lactobacillus) showed negative associations with the ADFI. Predicted function capacity analysis showed that the genes for amino acid biosynthesis had significantly different enrichment between pigs with high and low ADFI.
The present study provided important information on the profound effect of gut microbiota on porcine appetite and feeding behavior. This will profit us to regulate porcine appetite through modulating the gut microbiome in the pig industry.
Accumulating evidence shows that the gastric bacterial community may contribute to the development of gastric cancer (GC). However, the reported alterations of gastric microbiota were not always ...consistent among the literature. To assess reproducible signals in gastric microbiota during the progression of GC across studies, we performed a meta-analysis of nine publicly available 16S datasets with standard tools of the state-of-the-art. Despite study-specific batch effect, significant changes in the composition of the gastric microbiome were found during the progression of gastric carcinogenesis, especially when the Helicobacter pylori (HP) reads were removed from analyses to mitigate its compositional effect as they accounted for extremely large proportions of sequencing depths in many gastric samples. Differential microbes, including Fusobacterium, Leptotrichia, and several lactic acid bacteria such as Bifidobacterium, Lactobacillus, and Streptococcus anginosus, which were frequently and significantly enriched in GC patients compared with gastritis across studies, had good discriminatory capacity to distinguish GC samples from gastritis. Oral microbes were significantly enriched in GC compared to precancerous stages. Intriguingly, we observed mutual exclusivity of different HP species across studies. In addition, the comparison between gastric fluid and mucosal microbiome suggested their convergent dysbiosis during gastric disease progression. Taken together, our systematic analysis identified novel and consistent microbial patterns in gastric carcinogenesis.
More and more studies have indicated that gut microbiota takes part in the biosynthesis and metabolism of sex hormones. Inversely, sex hormones influence the composition of gut microbiota. However, ...whether microbiota in the gut and vagina is associated with estrus return of weaning sows is largely unknown. Here, using 16S rRNA gene sequencing in 158 fecal and 50 vaginal samples, we reported the shifts in the gut and vaginal microbiota between normal return and non-return sows. In fecal samples,
Lactobacillus
and S24-7 were enriched in normal return sows, while
Streptococcus luteciae
, Lachnospiraceae,
Clostridium
, and
Mogibacterium
had higher abundance in non-return sows. In vaginal swabs, the operational taxonomic units (OTUs) annotated to Clostridiales, Ruminoccaceae, and
Oscillospira
were enriched in normal return sows, while those OTUs annotated to
Campylobacter
,
Anaerococcus
,
Parvimonas
,
Finegoldia
, and
Dorea
had higher abundances in non-return sows. Co-abundance group (CAG) analysis repeated the identification of the bacterial taxa associated with the estrus return of weaning sows. The predicted functional capacities in both gut and vaginal microbiome were changed between normal return and non-return sows. Serum metabolome profiles were determined by non-targeted metabolome analysis in seven normal return and six non-return sows. The metabolite features having higher abundance in normal return sows were enriched in the pathways Steroid hormone biosynthesis, Starch and sucrose metabolism, Galactose metabolism, and Vitamin B6 metabolism, while the metabolite features belonging to organic acids and derivatives, indoles and derivatives, sulfoxides, and lignans and neolignans had significantly higher abundance in non-return sows. Correlation analysis found that the changes in gut microbiota were associated with the shifts of serum metabolites and suggested that certain bacteria might affect estrus return of weaning sow through serum metabolites. These findings may provide new insights for understanding the role of the gut and vaginal microbiota in sow return to estrus after weaning.
PMA (propidium monoazide) is one of the few methods that are compatible with metagenomic sequencing to characterize the live/intact microbiota. However, its efficiency in complex communities such as ...saliva and feces is still controversial. An effective method for depleting host and dead bacterial DNA in human microbiome samples is lacking. Here, we systematically evaluate the efficiency of osmotic lysis and PMAxx treatment (lyPMAxx) in characterizing the viable microbiome with four live/dead Gram+/Gram- microbial strains in simple synthetic and spiked-in complex communities. We show that lyPMAxx-quantitative PCR (qPCR)/sequencing eliminated more than 95% of the host and heat-killed microbial DNA and had a much smaller effect on the live microbes in both simple mock and spiked-in complex communities. The overall microbial load and the alpha diversity of the salivary and fecal microbiome were decreased by lyPMAxx, and the relative abundances of the microbes were changed. The relative abundances of
,
, and
in saliva were decreased by lyPMAxx, as was that of
in feces. We also found that the frequently used sample storage method, freezing with glycerol, killed or injured 65% and 94% of the living microbial cells in saliva and feces, respectively, with the
phylum affected most in saliva and the
and
phyla affected most in feces. By comparing the absolute abundance variation of the shared species among different sample types and individuals, we found that sample habitat and personal differences affected the response of microbial species to lyPMAxx and freezing.
The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes. PMA-qPCR was used to characterize the viable microbes in previous studies. However, its efficiency in complex communities such as saliva and feces is still controversial. By spiking-in four live/dead Gram+/Gram- bacterial strains, we demonstrate that lyPMAxx can effectively discriminate between live and dead microbes in the simple synthetic community and complex human microbial communities (saliva and feces). In addition, freezing storage was found to kill or injure the microbes in saliva and feces significantly, as measured with lyPMAxx-qPCR/sequencing. This method has a promising prospect in the viable/intact microbiota detection of complex human microbial communities.
Perinatal care is important in mammals due to its contribution to fetal growth, maternal health, and lactation. Substantial changes in host hormones, metabolism, and immunity around the parturition ...period may be accompanied by alterations in the gut microbiome. However, to our knowledge, changes in the gut microbiome and their contribution to the shifts in host metabolism around parturition have not been investigated in pigs. Furthermore, pigs are an ideal biomedical model for studying the interactions of the gut microbiota with host metabolism, due to the ease of controlling feeding conditions. Here we report dramatic remodeling of the gut microbiota and the potential functional capacity during the late stages of pregnancy (5 days before parturition, LP) to postpartum (within 6 h after delivery, PO) in both experimental and validated populations of sows (
n
= 107). The richness of bacteria in the gut of both pregnant and delivery sows significantly decreased, whilst the β-diversity dramatically expanded. The ratio of Bacteroidetes to Firmicutes, and the relative abundance of Prevotella significantly decreased, whilst the relative abundance of the predominant genus
Lactobacillus
significantly increased from LP to PO state. The predicted functional capacities of the gut microbiome related to amino acid metabolism, the metabolism of cofactors and vitamins, and glycan biosynthesis were significantly decreased from LP to PO state. However, the abundance of the functional capacities associated with carbohydrate and lipid metabolism were increased. Consistent with these changes, serum metabolites enriched at the LP stage were associated with the metabolism of amino acids and vitamins. In contrast, metabolites enriched at the PO stage were related to lipid metabolism. We further identified that the richness and β-diversity of the gut microbiota and the abundance of
Lactobacillus
accounted for shifts in the levels of bile acid metabolites associated with lipid metabolism. The results suggest that host-microbiota interactions during the perinatal period impact host metabolism. These benefit the lactation of sows by providing energy from lipid metabolism for milk production.
Germ-free models and bacterial transplantation technology facilitate the mechanism study of the host-gut microbe interaction. Among them, zebrafish is an economical and practical model with its ...characteristics, such as transparent larva and efficient gene manipulation, differing from the mouse. Here we enumerate the similarities and differences of the genes, the digestive tract structure and the gut microbiota of zebrafish and humans. And the recent reports on colonizing human gut microbes to zebrafish are elaborated. We summarize the advantages and limitations of this model and revalidate those with some important discoveries on the utilization of zebrafish in modeling human gut microbe research. This review will make the readers clear the advances in the application of zebrafish in gut microbiota-related researches.
•Zebrafish is an economical and practical model with transparent larva and efficient gene manipulation.•The standardized methodology for rearing germ-free zebrafish has been established, and it is cost-effective.•The digestive tract structure and homologous genes of zebrafish and humans were compared.•The gut microbiota composition of zebrafish and humans is different.•Some important researches studying the interaction of host and the gut microbiota were carried out based on this model.
Streptococcus mutans
appears to possess a sole iron-sulfur (Fe-S) cluster biosynthesis system encoded by the
sufCDSUB
cluster. This study was designed to examine the role of
sufCDSUB
in
S. mutans
...physiology. Allelic exchange mutants deficient of the whole
sufCDSUB
cluster and in individual genes were constructed. Compared to the wild-type, UA159, the
sufCDSUB
-deficient mutant, Δ
suf::kan
r
, had a significantly reduced growth rate, especially in medium with the absence of isoleucine, leucine or glutamate/glutamine, amino acids that require Fe-S clusters for biosynthesis and when grown with medium adjusted to pH 6.0 and under oxidative and nitrosative stress conditions. Relative to UA159, Δ
suf::kan
r
had major defects in stress tolerance responses with reduced survival rate of > 2-logs following incubation at low pH environment or after hydrogen peroxide challenge. When compared to UA159, Δ
suf::kan
r
tended to form aggregates in broth medium and accumulated significantly less biofilm. As shown by luciferase reporter fusion assays, the expression of
sufCDSUB
was elevated by > 5.4-fold when the reporter strain was transferred from iron sufficient medium to iron-limiting medium. Oxidative stress induced by methyl viologen increased
sufCDSUB
expression by > 2-fold, and incubation in a low pH environment led to reduction of
sufCDSUB
expression by > 7-fold. These results suggest that lacking of SufCDSUB in
S. mutans
causes major defects in various cellular processes of the deficient mutant, including growth, stress tolerance responses and biofilm formation. In addition, the viability of the deficient mutant also suggests that SUF, the sole Fe-S cluster machinery identified is non-essential in
S. mutans
, which is not known in any other bacterium lacking the NIF and/or ISC system. However, how the bacterium compensates the Fe-S deficiency and if any novel Fe-S assembly systems exist in this bacterium await further investigation.
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