Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig

Multi-strain probiotics attenuate carbohydrate-lipid metabolic dysregulation in type 2 diabetic rats via gut-liver axis modulation

Type 2 diabetes mellitus (T2DM) is a pervasive chronic metabolic disorder characterized by dysregulation of carbohydrate, protein, and lipid metabolism. The objective of this study was to elucidate the impact of multi-strain probiotic supplementation on the metabolism of carbohydrates and lipids and the interplay between the gut and liver in a T2DM rat model. A total of 32 rats were randomly assigned to four experimental groups: a control group, a T2DM model group, a low-dose probiotics group, and a high-dose probiotics group. The impact of probiotic intervention on glycemic and lipid profiles was evaluated, with a specific emphasis on the high-dose cohort. The treatment with multi-strain probiotics, consisting of three Lacticaseibacillus species and one Bifidobacterium species, resulted in a significant improvement in blood glucose and lipid profiles in T2DM rats, with the highest dosage demonstrating the most pronounced effects. Probiotic administration modulated gut microbiota composition and diversity, enriching potentially beneficial bacterial species and altering gut metabolic modules and carbohydrate-active enzyme profiles. Multi-omics analyses indicated that alterations in fecal short-chain fatty acids and serum bile acids may serve as pivotal mediators for crosstalk between hepatic and gut transcriptomic pathways. This study offers novel insights into the role of probiotics in managing T2DM via the gut-liver axis, emphasizing the potential of probiotic therapy in modulating key metabolic pathways.IMPORTANCEType 2 diabetes mellitus (T2DM) is a chronic metabolic disease characterized by hyperglycemia, caused by defects in insulin secretion, insulin action, or both. For individuals diagnosed with T2DM, managing diabetes-related complications is often the most challenging aspect. Exogenous probiotics have the potential to serve as a promising therapeutic strategy to improve diabetes-related symptoms. We conducted a 64-day animal experiment to investigate the effects of probiotics on T2DM-related metabolic disorders and dyslipidemia by feeding four mixed probiotics to T2DM rats. The results showed that probiotics exerted beneficial effects on glucose- and lipid-related homeostasis indices in diabetic rats to some extent and modulated the gut microbiota to manage T2DM via the gut-liver axis.

Multi-Enzyme Supplementation to Diets Containing 2 Protein Levels Affects Intramuscular Fat Content in Muscle and Modulates Cecal Microflora Without Affecting the Growth Performance of Finishing Pigs

We investigated the effects of crude protein (CP) levels and exogenous enzymes on growth performance, meat quality, toxic gas emissions, and colonic microbiota community in 200 finishing pigs. Four groups corresponded to 4 diets: 16.74% CP (high-protein level, HP) and 14.73% CP (medium protein level, MP) diet supplemented with or without 1-g/kg multi-enzymes (ENZs, including 1000-U/kg protease, 2500-U/kg α-amylase, and 10,000-U/kg β-glucanase), using a 2 × 2 factorial arrangement. After 7 weeks of trial, ENZs supplementation increased (P < 0.05) the average daily gain (ADG) of finishing pigs during weeks 4 to 7 and in the overall period and improved gross energy utilization. Dietary HP improved (P < 0.05) ADG during the overall period. The MP diet-treated pigs had higher intramuscular fat (IMF) content in the longissimus dorsi muscle (P < 0.01). ENZs supplementation to the MP diets lowered muscle IMF content (P < 0.01). Additionally, pigs fed the HP diet released (P < 0.05) more NH3 and H2S in excrement. The HP diet enhanced (P < 0.05) intestinal microbial richness, represented by higher observed_ amplicon sequence variants and Chao1. Administration of ENZs to the HP diet increased (P < 0.05) the Shannon and Pielou's evenness. Dietary MP promoted Firmicutes proliferation. Supplementary HP diet increased the relative abundances of Spirochaetota, Verrucomicrobiota, Desulfobacterota, and Fibrobacterota (P < 0.05). Supplemental ENZ elevated (P < 0.05) Actinobacteriota and Desulfobacterota abundances. ENZ supplementation to the HP diet increased the abundances of Bacteroidota, Desulfobacterota, and Proteobacteria but lowered their abundances in the MP diet. Taken together, the HP diet or ENZs' supplements improved growth performance. Although the interaction between CP levels and ENZs had no effect on growth performance, it modulated colonic flora and muscle IMF content.

Characterization of the diversity, genomic features, host bacteria, and distribution of crAss-like phages in the pig gut microbiome

Phages play an important role in shaping the gut microbiome. CrAss-like phages, which are key members of the gut virome, show high abundance in the human gut and have attracted increasing interest. However, few studies have been found in pigs, and the distribution of crAss-like phages across broader pig populations remains unknown. Here, we obtained 1,251 pig crAss-like phage genomes from 403 metagenomes publicly available and a pig gut virome dataset constructed by ourselves. These crAss-like phage genomes were further clustered into 533 virus operational taxonomic units (vOTUs). Phylogenetic analysis revealed that crAss-like phages in pig guts were distributed across four well-known family-level clusters (Alpha, Beta, Zeta, and Delta) but were absent in the Gamma and Epsilon clusters. Genomic structure analysis identified 149 pig crAss-like phage vOTUs that utilize alternative genetic codes. Gene blocks encoding replication and assembly proteins varied across crAss-like phage clusters. Approximately 64.73% of crAss-like phage genes lacked functional annotations, highlighting a gap in understanding their functional potential. Numerous anti-CRISPR protein genes were identified in crAss-like phage genomes, and CAZymes encoded by these phages were primarily lysozymes. Host prediction indicated that bacterial hosts of pig crAss-like phages primarily belonged to Prevotella, Parabacteroides, and UBA4372. We observed that interactions between crAss-like phages and Prevotella copri might have a possible effect on fat deposition in pigs. Finally, all detected vOTUs exhibited low prevalence across pig populations, suggesting heterogeneity in crAss-like phage compositions. This study provides key resources and novel insights for investigating crAss-like phage-bacteria interactions and benefits research on the effects of crAss-like phages on pig health and production traits.

Multi-Omics Analysis Reveals the Negative Effects of High-Concentrate Diets on the Colonic Epithelium of Dumont Lambs

Feeding HC diets has been found to induce metabolic dysregulation in the colon. However, the mechanisms by which changes in colonic flora and metabolites damage the colonic epithelium are poorly studied. Therefore, the present experiment used a multi-omics technique to investigate the mechanism of colonic injury induced by high-concentrate diets in lambs. Twelve male Dumont lambs were randomly split into two groups: a low-concentrate diet (LC = concentrate/forage = 30:70) group and a high-concentrate diet (HC = concentrate/forage = 70:30) group. The results showed that the HC group presented significantly increased lipopolysaccharide (LPS) concentrations in the colonic epithelium and significantly decreased serum total cholesterol (TC), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) levels (p < 0.05), which led to cavities and inflammatory cell infiltration in the colonic epithelium. The HC group had significantly lower pH and less VFAs in colon contents, as well as a significantly increased abundance of bacteria of the genera [Eubacterium]_coprostanoligenes_group, Rikenellaceae_RC9_gut_group, Treponema, Clostridia_UCG-014, Alistipes, Ruminococcus, Christensenellaceae_R-7_group, UCG-002, Bacteroidales_RF16_group and Lachnospiraceae_AC2044_group compared to the LC diet group. These microorganisms significantly increased the level of metabolites of cholic acid, chenodeoxycholic acid, LysoPA (P-16:0/0:0), methapyrilene, and fusaric acid. A transcriptome analysis showed that cytokine-cytokine receptor interaction, glutathione metabolism, and the peroxisome signaling pathway were downregulated in the colon epithelium of the lambs fed the HC diet. Therefore, the HC diet caused epithelial inflammation and oxidative damage by affecting the interaction between the microbial flora of the colon and metabolites and the host epithelium, which eventually disrupted colon homeostasis and had a negative impact on sheep health.

Complete genome analysis of Bacillus velezensis HF-14,109 with potential for broad-spectrum antimicrobial activity and high enzyme-producing ability from common carp (Cyprinus carpio L.)

Bacillus velezensis (B. velezensis) HF-14,109 is an aerobic Gram-positive bacterium isolated from the gut of healthy carp (Cyprinus carpio L.). Here, we sequenced and annotated the genome of HF-14,109, identified and classified its enzyme-producing genes and secondary metabolite biosynthesis gene clusters (BGCs), and verified the inhibitory effects on pathogenic bacteria in vitro. Results suggested that HF-14,109 had a circular 4,214,172 bp genome that contains 4,392 predicted genes with an average length and GC content of 851.56 bp and 46.94%, respectively. A total of 210 non-coding RNAs, 8 CRISPR sequences, and 152 tandem repeats were predicted. Based on a CAZy database analysis, HF-14,109 contains 93 genes encoding enzymes for carbohydrate-related processes, 38 of which were glycoside hydrolase genes and divided into 20 families. Based on enzyme predictions, HF-14,109 had the capability to hydrolyze high molecular carbohydrates such as starch, disaccharides such as lactose and sucrose, and non-starch polysaccharides such as β-glucan, mannan, fructan and xylan. Twelve BGCs for producting secondary metabolites were identified by antiSMASH analysis, 5 of which were predicted to encode polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs), indicating that HF-14,109 could produce multiple secondary metabolites. The genome of HF-14,109 contained numerous genes encoding glycoside hydrolases and BGCs for producting secondary metabolites. Besides, the HF-14,109 could inhibit pathogenic bacteria such as E. tarda, A. hydrophila, S. aurenus, and E. coli in vitro. In conclusion, our results demonstrate that HF-14,109 has the effects of hydrolyzing non-starch polysaccharides and inhibiting pathogenic bacteria, which lays a solid foundation for elucidating its antibacterial and enzyme-producing mechanisms, and is expected to be developed as a probiotic for aquaculture feed in the future.

Synergistic effects of multi-enzyme supplementation on nutrient digestion and absorption in the foregut and hindgut

This study was conducted to investigate the effect of dietary multi-enzyme (MCPC) supplementation on synergistically enhancing the functions of both the foregut and hindgut, ultimately improving the nutrient digestion and utilization throughout the gastrointestinal tract. In vitro results demonstrated that MCPC increased the phosphorus and reducing sugar levels in the supernatant during enzymatic hydrolysis. Furthermore, during the fermentation of the enzymatic hydrolysis products, MCPC significantly increased the FRD0 value of the enzymatic hydrolysis products from both the positive control (PC) and negative control 1 (NC1) diets (p < 0.05). MCPC reduced the T1/2 value of in vitro fermentation products from the PC diet (p < 0.01), and decreased the VF (p = 0.082) and K (p < 0.05) values for the NC1 diet. Additionally, 72 crossbred barrows [Duroc × (Landrace × Yorkshire)], weighing 25 kg, were fed one of six diets until their live weight approached 50 kg. The basal diets consisted of PC, NC1 and negative control 2 (NC2), while the remaining three diets were prepared by adding 100 mg/kg MCPC to the respective basal diets. The results showed that MCPC supplementation significantly upregulated the expression of solute carrier family 17 member 4 (SLC17A4) and vitamin D receptor (VDR) genes in the duodenum (p < 0.05), while downregulating the expression of Calbindin-D28k (CaBP-D28K) and solute carrier family 1 member 4 (SLC1A4) genes (p < 0.05) in growing pigs. Moreover, MCPC supplementation significantly upregulated the expression of VDR, glucose transporter 2 (GLUT2) and intestinal fatty acid binding protein (FABP2) genes in the jejunum of growing pigs. Furthermore, MCPC supplementation significantly increased the relative abundances of Bacteroidota, Prevotella and Phascolarctobacterium (p < 0.05), while reducing the relative abundances of Verrucomicrobiota and Clostridium_sensu_stricto_1 (p < 0.05) in the colon of growing pigs. In conclusion, MCPC enhances nutrient digestion and absorption in the foregut, provides fermentable substrates for hindgut microbial fermentation, and improves gut microbiota composition. This improves hindgut fermentation and supports the synergistic interaction between the foregut and hindgut, ultimately improving nutrient utilization and benefiting animal health.

Superior ability of dietary fiber utilization in obese breed pigs linked to gut microbial hydrogenotrophy

Dietary fiber is widely recognized for its benefits to human health. Individual variations in the ability to degrade dietary fiber are influenced by the gut microbiome that may be associated with the host's metabolic phenotype and genetic diversity. This is exemplified by the distinct fiber digestibility observed in obese (e.g. Meishan) and lean-breed (e.g. Yorkshire) pigs. However, the underlying mechanisms remain unclear. The present study found that with the same diet under the same environment, the obese-type Meishan pigs showed greater dietary fiber digestibility and harbored higher abundances of polysaccharide-degrading bacteria (Bacteroides, Treponema, and Paraprevotella) compared to lean-type Yorkshire pigs. Metatranscriptomic profiling revealed that the elevated presence of Bacteroides contributed to the enrichment of carbohydrate-active enzymes, particularly those degrading arabinoxylan, indicating a preference for arabinoxylan as a substrate in Meishan pigs. Further enzymatic-product measurements, combined with microbial enzyme profiles, validated greater microbial conversion of xylose into short-chain fatty acids (SCFAs) in Meishan pigs. Additionally, higher abundances of hydrogenotrophic microbes (Methanobrevibacter and Blautia) were detected in the Meishan gut, along with the enrichment of methanogenesis and acetogenesis pathways. To determine whether methanogenesis drives inter-breed variation in arabinoxylan degradation, an in vitro experiment using the methanogen inhibitor, 2-bromoethanesulfonate (BES) was performed. The results confirmed that Meishan gut microbiome effectively reduced hydrogen accumulation through methanogenesis, promoting arabinoxylan degradation. Conversely, inhibiting methanogenesis by BES led to hydrogen accumulation, reduced SCFAs, β-xylosidase activity, and Bacteroides abundances. These findings demonstrate that the Meishan pigs have a superior ability of dietary fiber utilization with greater microbial conversion to more SCFAs, which is linked to stronger hydrogenotrophic methanogenesis. This study reinforces the role of gut microbial hydrogenotrophy in dietary fiber utilization in pigs.

Division mechanism of labor in Diqing Tibetan Pigs gut microbiota for dietary fiber efficiently utilization

The Diqing Tibetan (TP) pig is an roughage tolerance breed that inhabits an area with the highest altitude distribution in the world and can be maintained on a diet containing 90 % forage material in confined production systems. Our results showed that TP pigs had a strong capability for high-efficiency utilization of arabinose and xylose. Metagenomic analysis revealed that the secretion of carbohydrate esterases was mainly undertaken by fecal strains of Microbacterium, Alistipes, Acinetobacter, and Faecalibacterium, while Microbacterium, Prevotella, Turicibacter, Lactobacillus, Clostridium, and Streptococcus were responsible for most of the secretion of glycoside hydrolases. Then, a brand new species, which was named Microbacterium sp. Qiao 01 was captured and appeared to have the highest fiber utilization ability in vitro, degrading 36.54 % of the neutral detergent fiber in corn stover. Our results provide strong evidence that efficient utilization of dietary fiber by TP pigs is due to the emergence of highly specialized microbial strategies in the gut. Microorganisms showed preferences and a clear division of labor in the degradation process of dietary fiber. This study has great practical significance for improving the utilization efficiency of livestock feed and alleviating the tension of food insecurity.

Secondary bile acids are associated with body lipid accumulation in obese pigs

The aim of this study was to investigate the reasons for the differences in lipid accumulation between lean and obese pigs. The bile acids with varying levels within two types of pigs were found and then in vitro experiments were conducted to identify whether these bile acids can directly affect lipid accumulation. Fourteen pigs, including seven lean and seven obese pigs with body weights of approximately 80 kg, were fed the same diet at an amount approximately equivalent to 3% of their respective body weights daily for 42 d. In vitro, 3T3-L1 preadipocytes were cultured in medium with high glucose levels and were differentiated into mature adipocytes using differentiation medium. Then, bile acids were added to mature adipocytes for 4 d. The results showed that there was a difference in body lipids levels and gut microbiota composition between obese and lean pigs (P < 0.05). According to the results of gut microbial function prediction, the bile acid biosynthesis in colonic digesta of obese pigs were different from that in lean pig. Sixty-five bile acids were further screened by metabolomics, of which 4 were upregulated (P < 0.05) and 2 were downregulated (P < 0.05) in obese pigs compared to lean pigs. The results of the correlation analysis demonstrated that chenodeoxycholic acid-3-β-D-glucuronide (CDCA-3Gln) and ω-muricholic acid (ω-MCA) had a negative correlation with abdominal fat weight and abdominal fat rate, while isoallolithocholic acid (IALCA) was positively associated with crude fat in the liver and abdominal fat rate. There was a positive correlation between loin muscle area and CDCA-3Gln and ω-MCA (P < 0.05), however, IALCA and 3-oxodeoxycholic acid (3-oxo-DCA) were negatively associated with loin eye muscle area (P < 0.05). Isoallolithocholic acid increased the gene expression of peroxisome proliferator-activated receptor gamma (PPARG) and the number of lipid droplets (P < 0.05), promoting the lipid storage when IALCA was added to 3T3-L1 mature adipocytes in vitro. In conclusion, the concentration of bile acids, especially gut microbiota related-secondary bile acids, in obese pigs was different from that in lean pigs, which may contribute to lipid accumulation within obese pigs.

Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle

Metagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

Maternal supplementation with konjac glucomannan improves maternal microbiota for healthier offspring during lactation

BACKGROUND

The maternal diet during gestation and lactation affects the health of the offspring. Konjac glucomannan (KGM) is a significantly functional polysaccharide in food research, possessing both antioxidant and prebiotic properties. However, the mechanisms of how KGM regulates maternal nutrition remain insufficient and limited. This study aimed to investigate maternal supplementation with KGM during late gestation and lactation to benefit both maternal and offspring generations.

RESULTS

Our findings indicate that KGM improves serum low density lipoprotein cholesterol (LDL-C) and antioxidant capacity. Furthermore, the KGM group displayed a significant increase in the feed intake-related hormones neuropeptide tyrosine (NPY), Ghrelin, and adenosine monophosphate-activated kinase (AMPK) levels. KGM modified the relative abundance of Clostridium, Candidatus Saccharimonas, unclassified Firmicutes, and unclassified Christensenellaceae in sow feces. Acetate, valerate, and isobutyrate were also improved in the feces of sows in the KGM group. These are potential target bacterial genera that may modulate the host's health. Furthermore, Spearman's correlation analysis unveiled significant correlations between the altered bacteria genus and feed intake-related hormones. More importantly, KGM reduced interleukin-6 (IL-6) levels in milk, further improved IL-10 levels, and reduced zonulin levels in the serum of offspring.

CONCLUSION

In conclusion, maternal dietary supplementation with KGM during late gestation and lactation improves maternal nutritional status by modifying maternal microbial and increasing lactation feed intake, which benefits the anti-inflammatory capacity of the offspring serum. © 2024 Society of Chemical Industry.

Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment

Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00192-z.

Viral AMGs-driven pentose phosphate pathway in natural wetland

Viruses exist anywhere on earth where there is life, and among them, virus-encoded auxiliary metabolic genes (AMGs) can maintain ecosystem balance and play a major role in the global ecosystem. Although the function of AMGs has been widely reported, the genetic diversity of AMGs in natural ecosystems is still poorly understood. Exploring the genetic diversity of viral community-wide AMGs is essential to gain insight into the complex interactions between viruses and hosts. In this article, we studied the phylogenetic tree, principal co-ordinates analysis (PCoA), α diversity, and metabolic pathways of viral auxiliary metabolism genes involved in the pentose phosphate pathway (PPP) through metagenomics, and the changes of metabolites and genes of host bacteria were further studied by using Pseudomonas mandelii SW-3 and its lytic phage based on metabolic flow and AMGs expression. We found that the viral AMGs in the Napahai plateau wetland were created by a combination of various external forces, which contributed to the rich genetic diversity, uniqueness, and differences of the virus, which promoted the reproduction of offspring and better adaptation to the environment. Overall, this study systematically describes the genetic diversity of AMGs associated with the PPP in plateau wetland ecosystems and further expands the understanding of phage-host unique interactions.

Novel primers to identify a wider diversity of butyrate-producing bacteria

Butyrate-producing bacteria are a functionally important part of the intestinal tract flora, and the resulting butyric acid is essential for maintaining host intestinal health, regulating the immune system, and influencing energy metabolism. However, butyrate-producing bacteria have not been defined as a coherent phylogenetic group. They are primarily identified using primers for key genes in the butyrate-producing pathway, and their use has been limited to the Bacillota and Bacteroidetes phyla. To overcome this limitation, we developed functional gene primers able to identify butyrate-producing bacteria through the butyrate kinase gene, which encodes the enzyme involved in the final step of the butyrate-producing pathway. Genomes extracted from human and rat feces were used to amplify the target genes through PCR. The obtained sequences were analyzed using BLASTX to construct a developmental tree using the MEGA software. The newly designed butyrate kinase gene primers allowed to recognize a wider diversity of butyrate-producing bacteria than that recognized using currently available primers. Specifically, butyrate-producing bacteria from the Synergistota and Spirochaetota phyla were identified for the first time using these primers. Thus, the developed primers provide a more accurate method for researchers and doctors to identify potential butyrate-producing bacteria and deepen our understanding of butyrate-producing bacterial species.

Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model

Signal peptides (SPs) are essential to target and transfer transmembrane and secreted proteins to the correct positions. Many existing computational tools for predicting SPs disregard the extreme data imbalance problem and rely on additional group information of proteins. Here we introduce Unbiased Organism-agnostic Signal Peptide Network (USPNet), an SP classification and cleavage-site prediction deep learning method. Extensive experimental results show that USPNet substantially outperforms previous methods on classification performance by 10%. An SP-discovering pipeline with USPNet is designed to explore unprecedented SPs from metagenomic data. It reveals 347 SP candidates, with the lowest sequence identity between our candidates and the closest SP in the training dataset at only 13%. In addition, the template modeling scores between candidates and SPs in the training set are mostly above 0.8. The results showcase that USPNet has learnt the SP structure with raw amino acid sequences and the large protein language model, thereby enabling the discovery of unknown SPs.

Comparative evaluation of the fecal microbiota of adult hybrid pigs and Tibetan pigs, and dynamic changes in the fecal microbiota of hybrid pigs

The breed of pig can affect the diversity and composition of fecal microbiota, but there is a lack of research on the fecal microbiota of hybrid pigs. In this study, feces samples from Chuanxiang black pigs (a hybrid of Tibetan and Duroc pigs) aged 3 days (n = 24), 70 days (n = 31), 10 months (n = 13) and 2 years (n = 30) and Tibetan pigs aged 10 months (n = 14) and 2 years (n = 15) were collected and sequenced by 16S rRNA gene sequencing technology. We also measured the weight of all the tested pigs and found that the 10-month-old and two-year-old Chuanxiang black pigs weighed about three times the weight of Tibetan pigs of the same age. After comparing the genus-level microbiota composition of Tibetan pigs and Chuanxiang black pigs at 10 months and two years of age, we found that Treponema and Streptococcus were the two most abundant bacteria in Chuanxiang black pigs, while Treponema and Chirstensenellaceae_R.7_group were the two most abundant bacteria in Tibetan pigs. Prediction of microbial community function in adult Chuanxiang black pigs and Tibetan pigs showed changes in nutrient absorption, disease resistance, and coarse feeding tolerance. In addition, we also studied the changes in fecal microbiota in Chuanxiang black pigs at 3 days, 70 days, 10 months, and 2 years of age. We found that the ecologically dominant bacteria in fecal microbiota of Chuanxiang black pigs changed across developmental stages. For example, the highest relative abundance of 70-day-old Chuanxiang black pigs at the genus level was Prevotella. We identified specific microbiota with high abundance at different ages for Chuanxiang black pigs, and revealed that the potential functions of these specific microbiota were related to the dominant phenotype such as fast growth rate and strong disease resistance. Our findings help to expand the understanding of the fecal microbiota of hybrid pigs and provide a reference for future breeding and management of hybrid pigs.

Underestimated health risks: Dietary restriction magnify the intestinal barrier dysfunction and liver injury in mice induced by polystyrene microplastics

Microplastics (MPs) have gained significant attention due to their widespread presence in the environment. While studies have been conducted to investigate the risks associated with MPs, the potential effects of MPs on populations with varying dietary habits, such as dietary restriction (DR), remain largely undefined. The sensitivity of the body to invasive contaminants may increase due to insufficient food intake. Here, we aimed to investigate whether dietary restriction could affect the toxicity of MPs in mice. Following a 5-week exposure to 200 μg/L polystyrene microplastics (PSMPs), DR-PSMPs treatment group exhibited significant intestinal barrier dysfunction compared to ND-PSMPs treatment group, as determined by histopathological and biochemical analysis. Dietary restriction worsened liver oxidative stress and bile acid disorder in mice exposed to PSMPs. 16S rRNA sequencing analysis revealed that DR-PSMPs treatment caused alterations in gut microbiota composition, including the downregulation of probiotics abundance and upregulation of pathogenic bacteria abundance. The negative effects caused by PSMPs in mice with dietary restriction could attribute to increased MPs bioaccumulation, declined water intake, reduced probiotics abundance, and elevated pathogenic bacteria abundance, as well as the susceptibility of the dietary restriction individual. Our findings hint that the biological effects of contaminants could be affected by dietary habits.

Probiotics alleviate constipation and inflammation in late gestating and lactating sows

Constipation and systemic inflammation are common in late pregnant and lactating sows, which cause health problems like uteritis, mastitis, dystocia, or even stillbirth, further influencing piglets' survival and growth. Probiotic supplementation can improve such issues, but the beneficial mechanism of relieving constipation and enhancing gut motility remains underexplored. This study aimed to investigate the effects and mechanism of probiotic supplementation in drinking water to late pregnant sows on constipation, inflammation, and piglets' growth performance. Seventy-four sows were randomly allocated to probiotic (n = 36) and control (n = 38) groups. Probiotic treatment significantly relieved sow constipation, enhanced serum IL-4 and IL-10 levels while reducing serum IL-1β, IL-12p40, and TNF-α levels, and increased piglet daily gain and weaning weight. Furthermore, probiotic administration reshaped the sow gut bacteriome and phageome structure/diversity, accompanied by increases in some potentially beneficial bacteria. At 113 days of gestation, the probiotic group was enriched in several gut microbial bioactive metabolites, multiple carbohydrate-active enzymes that degrade pectin and starch, fecal butyrate and acetate, and some serum metabolites involved in vitamin and amino acid metabolism. Our integrated correlation network analysis revealed that the alleviation of constipation and inflammation was associated with changes in the sow gut bacteriome, phageome, bioactive metabolic potential, and metabolism.

Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea

BACKGROUND

Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination.

RESULTS

We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.

Gut microbiome signatures of extreme environment adaption in Tibetan pig

Tibetan pigs (TPs) can adapt to the extreme environments in the Tibetan plateau implicated by their self-genome signals, but little is known about roles of the gut microbiota in the host adaption. Here, we reconstructed 8210 metagenome-assembled genomes from TPs (n = 65) living in high-altitude and low-altitude captive pigs (87 from China-CPs and 200 from Europe-EPs) that were clustered into 1050 species-level genome bins (SGBs) at the threshold of 95% average nucleotide identity. 73.47% of SGBs represented new species. The gut microbial community structure analysis based on 1,048 SGBs showed that TPs was significantly different from low-altitude captive pigs. TP-associated SGBs enabled to digest multiple complex polysaccharides, including cellulose, hemicellulose, chitin and pectin. Especially, we found TPs showed the most common enrichment of phyla Fibrobacterota and Elusimicrobia, which were involved in the productions of short- and medium-chain fatty acids (acetic acid, butanoate and propanoate; octanomic, decanoic and dodecanoic acids), as well as in the biosynthesis of lactate, 20 essential amino acids, multiple B vitamins (B1, B2, B3, B5, B7 and B9) and cofactors. Unexpectedly, Fibrobacterota solely showed powerful metabolic capacity, including the synthesis of acetic acid, alanine, histidine, arginine, tryptophan, serine, threonine, valine, B2, B5, B9, heme and tetrahydrofolate. These metabolites might contribute to host adaptation to high-altitude, such as energy harvesting and resistance against hypoxia and ultraviolet radiation. This study provides insights into understanding the role of gut microbiome played in mammalian high-altitude adaptation and discovers some potential microbes as probiotics for improving animal health.

Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity

Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism.

Characterization, estimation of virulence and drug resistance of diarrheagenic escherichia coli (DEC) isolated from Tibetan pigs

In this study, we collected feces of Tibetan piglets from Nyingchi area for isolation, culture, identification, virulence gene analysis and drug resistance analysis of Escherichia Coli. The results demonstrated a 41.3% isolation rate of Diarrheagenic Escherichia Coli from Tibetan pigs with the main phylogenetic groups: group A (68.6%) and group B2 (15.7%). Typical E.coli accounted for 76.5%. The highest detection rates of porcine virulence genes were E.coli heat-resistant enterotoxin STb (58.82%) and F107 fimbrial subunit (23.53%). The highest detection rates of virulence genes from Tibetan pigs were fimC (80.39%) and ompA (76.47%). A drug sensitivity test showed that Diarrheagenic Escherichia Coli from Tibetan pigs had high drug resistance rates to mezlocillin, doxycycline and gentamicin. This study comprehensively analyzed the species composition, virulence and drug resistance of Diarrheagenic Escherichia Coli from Tibetan pigs, which provided a clearer and more targeted idea for the prevention and treatment of yellow and white dysentery in Tibetan pigs in the future.

Trait biases in microbial reference genomes

Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.

Comparison of the characteristics of gut microbiota response to lead in Bufo gargarizans tadpole at different developmental stages

In amphibians, lead (Pb) exposure could alter the composition and structure of gut microbiota, but changes involving microbiota of several successive phases following Pb exposure have been less studied. In the present study, we compared the effects of Pb exposure on morphological parameters and gut microbiota of Bufo gargarizans at Gosner stage (Gs) 33, Gs36, and Gs42. Our results showed that total length (TL), snout-vent length (SVL), and body wet weight (TW) of B. gargarizans at Gs33, as well as TL and SVL at Gs42, were significantly increased after Pb exposure. In addition, high-throughput sequencing analysis indicated that gut microbiota has distinct responses to Pb exposure at different developmental stages. The diversity of gut microbiota was significantly reduced under Pb exposure at Gs33, while it was significantly increased at Gs42. In terms of community composition, Spirochaetota, Armatimonadota, and Patescibacteria appeared in the control groups at Gs42, but not after Pb treatment. Furthermore, functional prediction indicated that the relative abundance of metabolism pathway was significantly decreased at Gs33 and Gs36, and significantly increased at Gs42. Our results fill an important knowledge gap and provide comparative information on the gut microbiota of tadpoles at different developmental stages following Pb exposure.

Effect of Energy Provision Strategy on Rumen Fermentation Characteristics, Bacterial Diversity and Community Composition

This study was conducted to explore the rumen fermentation characteristics, bacterial diversity, and community composition of Hu sheep under four energy provision strategies. Ninety-six Hu sheep (body weight: 17.78 ± 1.24 kg) were equally assigned to four energy provision strategies: (1) low-energy diet for the whole finishing stage (LL); (2) high-energy diet for the whole finishing stage (HH); (3) low-energy diet in the early finishing stage and high-energy diet in the late finishing stage (LH); (4) high-energy diet in the early finishing stage and low-energy diet in the late finishing stage (HL). The results showed that the proportion of acetate was lower in the HH group than that in the HL group, whereas the opposite result was observed for the butyrate proportion (p < 0.05). The Chao 1, observed species, PD whole tree, and Shannon index of the rumen bacteria were higher in the LL group than that in the HH group (p < 0.05). The taxonomic annotations revealed that the Patescibacteria, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Anaeroplasma abundances were higher in the HL group than that in the HH group, and the opposite results were observed regarding the relative abundances of Selenomonas and Anaerovibrio (p < 0.05). The relative abundances of Spirochaetota and Treponema were higher in the LH group than that in the HH group (p < 0.05). Moreover, the analysis of similarity (ANOSIM) showed significant differences between groups (R = 0.6792 and p = 0.001). This study indicates that the energy provision strategy had little impact on the rumen fermentation characteristics, while it heavily affected the rumen bacterial diversity and community composition. This study may provide insight into the rumen fermentation characteristics and bacterial community under routine finishing models and contribute to the optimization of energy provision strategies of Hu sheep.

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts

BACKGROUND

Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments.

RESULTS

Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders.

CONCLUSIONS

Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract.

Alterations in gut microbiota improve SCFA production and fiber utilization in Tibetan pigs fed alfalfa diet

Tibetan pigs were thought to have good performances of rough feeding tolerance, which may be related to the gut microbiota. This study was conducted to investigate the changes of colonic microbiota contribute to fiber utilization in Tibetan pigs fed alfalfa supplementation diet compared with basal diet, and verified whether the microbial community in Tibetan pigs fed alfalfa diet was beneficial to utilize fiber using in vitro fermentation. A total of 40 Tibetan pigs were allocated into two groups and fed with a corn-soybean meal basal diet (CD) or a 50% alfalfa supplementation diet (AD) for 42d. Our results showed pigs fed CD diet improved carcass weight compared to pigs fed AD diet (p < 0.05), yet reduced the bacterial diversity (p < 0.05). Tibetan pigs fed CD diet increased certain pathogenic bacteria (Streptococcus) abundance (FDR < 0.05). Alfalfa consumption increased fiber-degrading bacteria abundance (UCG-005, Rikenellaceae_RC9_gut_group, Prevotellaceae_UCG-003, Alloprevotella, Marvinbryantia, and Anaerovibrio) in the colonic digesta (FDR < 0.05) and improved concentrations of acetate, propionate, butyrate, and total SCFA in colonic content (p < 0.05). Higher fermentation capacity of fecal microbiota from pig fed AD diet was verified by in vitro fermentation. Collectively, our results indicated that alfalfa supplementation in diets improved the abundance of fiber-degrading bacteria and SCFA production in the hindgut of Tibetan pig, as well as enhanced the fermentation capacity of fecal microbiota.

Fermented soybean meal modified the rumen microbiome to enhance the yield of milk components in Holstein cows

The study was conducted to evaluate the rumen microbiota as well as the milk composition and milk component yields of Holstein cows supplemented with fermented soybean meal (FSBM). Eighteen Holstein cows in their 2nd parity with 54.38 ± 11.12 SD days in milking (DIM) were divided into two dietary groups (CON and TRT) of nine cows per group. The cows in the TRT group received 300 g of FSBM per cow per day in addition to the conventional diet, while each cow in the CON group was supplemented with 350 g of soybean meal (SBM) in their diet daily throughout the 28-day feeding trial. Rumen bacterial composition was detected via 16S rRNA sequencing, and the functional profiles of bacterial communities were predicted. Milk composition, milk yield, as well as rumen fermentation parameters, and serum biochemistry were also recorded. The inclusion of FSBM into the diets of Holstein cows increased the milk urea nitrogen (MUN), milk protein yield, fat corrected milk (FCM), and milk fat yield while the milk somatic cell count (SCC) was decreased. In the rumen, the relative abundances of Fibrobacterota, and Spirochaetota phyla were increased in the TRT group, while the percentage of Proteobacteria was lower. In addition, the supplementation of FSBM to Holstein cows increased the acetate percentage, rumen pH, and acetate to propionate ratio, while the proportion of propionate and propionate % was observed to decrease in the TRT group. The KEGG pathway and functional prediction revealed an upregulation in the functional genes associated with the biosynthesis of amino acids in the TRT group. This enrichment in functional genes resulted in an improved synthesis of several essential amino acids including lysine, methionine, and branch chain amino acids (BCAA) which might be responsible for the increased milk protein yield. Future studies should employ shotgun metagenomics, transcriptomics, and metabolomics technology to investigate the effects of FSBM on other rumen microbiomes and milk protein synthesis in the mammary gland in Holstein cows. KEY POINTS: • The supplementation of fermented soybean meal (FSBM) to Holstein cows modified the proportion of rumen bacteria. • Predicted metabolic pathways and functional genes of rumen bacteria revealed an enrichment in pathway and genes associated with biosynthesis of amino acids in the group fed FSBM. • The cows supplemented with FSBM record an improved rumen fermentation. • Cows supplemented with FSBM recorded an increased yield of milk protein and milk fat.

Effects of fecal microbiota transplantation from yaks on weaning diarrhea, fecal microbiota composition, microbial network structure and functional pathways in Chinese Holstein calves

This study was conducted to investigate the effect of fecal microbiota transplantation (FMT) from yaks on weaning diarrhea, fecal microbiota composition, microbial network structure and functional pathways in Chinese Holstein Calves. In this study, 50 calves were randomly divided into five groups of 10 each: NC group (no supplementation), Control group (normal saline), low concentration FMT group (LFMT, 1 × 108 CFU/ml), high concentration FMT group (HMFT, 1 × 109 CFU/ml), and sterilized FMT group (SMFT, sterilized bacterial solution). The test lasted for 30 days. We found that FMT reduced the incidence of diarrhea in weaned calves, and the anti-diarrhea effect of LFMT was stronger than those of HFMT and SFMT. Calf feces were collected by rectal palpation on days 5, 10, 15, and 20 post-weaning, and high-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer region of fecal microbiota was performed. We observed that the richness and diversity of bacterial microbiota in the LFMT, HFMT, and SFMT groups were higher than those in the NC and Control groups at day 20 after weaning. The treatment had a significant effect on bacterial richness (p < 0.05), but not on fungal diversity or richness. The analysis of gut microbiome showed that Firmicutes and Bacteroides were the main bacterial phyla in the feces of weaned calves, and norank_ f Muribaculaceae, UCG-005, Rikenellaceae_RC9_gut_group, Bacteroides, and Blautia were the main genera. Ascomycota and Basidiomycota were the main fungal phyla. Compared to abundance parameters in the Control and NC groups, relative abundances of Firmicutes in the FMT groups increased at different time points after weaning. The relative abundance of Blautia and Lactobacillus in the LFMT group increased significantly after weaning. In addition, abundances of Ruminococcus and Romboutsia, which produce short-chain fatty acids, were also increased in different FMT groups. FMT significantly increased the relative abundance of beneficial bacteria, enhanced the complexity of the fecal microbial network, and promoted important metabolic and cellular processes in weaned calves. In conclusion, our study provides a reference and theoretical basis for FMT to prevent calf weaning diarrhea and other intestinal diseases in ruminants.

Impact of Clarified Apple Juices with Different Processing Methods on Gut Microbiota and Metabolomics of Rats

The consumption of processed foods has increased compared to that of fresh foods in recent years, especially due to the coronavirus disease 2019 pandemic. Here, we evaluated the health effects of clarified apple juices (CAJs, devoid of pectin and additives) processed to different degrees, including not-from-concentrate (NFC) and from-concentrate (FC) CAJs. A 56-day experiment including a juice-switch after 28 days was designed. An integrated analysis of 16S rRNA sequencing and untargeted metabolomics of cecal content were performed. In addition, differences in the CAJs tested with respect to nutritional indices and composition of small-molecule compounds were analyzed. The NFC CAJ, which showed a higher phenolic content resulting from the lower processing degree, could improve microbiota diversity and influence its structure. It also reduced bile acid and bilirubin contents, as well as inhibited the microbial metabolism of tryptophan in the gut. However, we found that these effects diminished with time by performing experiment extension and undertaking juice-switching. Our study provides evidence regarding the health effects of processed foods that can potentially be applied to public health policy decision making. We believe that NFC juices with a lower processing degree could potentially be healthier than FC juice.

MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads

MOTIVATION

Metagenome-assembled genomes (MAGs) have substantially extended our understanding of microbial functionality. However, 16S rRNA genes, which are commonly used in phylogenetic analysis and environmental surveys, are often missing from MAGs. Here, we developed MarkerMAG, a pipeline that links 16S rRNA genes to MAGs using paired-end sequencing reads.

RESULTS

Assessment of MarkerMAG on three benchmarking metagenomic datasets with various degrees of complexity shows substantial increases in the number of MAGs with 16S rRNA genes and a 100% assignment accuracy. MarkerMAG also estimates the copy number of 16S rRNA genes in MAGs with high accuracy. Assessments on three real metagenomic datasets demonstrates 1.1- to 14.2-fold increases in the number of MAGs with 16S rRNA genes. We also show that MarkerMAG-improved MAGs increase the accuracy of functional prediction from 16S rRNA gene amplicon data. MarkerMAG is helpful in connecting information in MAG database with those in 16S rRNA databases and surveys and hence contributes to our increasing understanding of microbial diversity, function, and phylogeny.

AVAILABILITY

MarkerMAG is implemented in Python3 and freely available at https://github.com/songweizhi/MarkerMAG.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Generation and application of pseudo-long reads for metagenome assembly

BACKGROUND

Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads.

RESULTS

In this study, we present a new method called PLR-GEN. It creates pseudo-long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo-long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo-long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes.

CONCLUSIONS

PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.

Selective Maternal Seeding and Rearing Environment From Birth to Weaning Shape the Developing Piglet Gut Microbiome

The acquisition and development of the mammalian microbiome early in life are critical to establish a healthy host-microbiome symbiosis. Despite recent advances in understanding microbial sources in infants, the relative contribution of various microbial sources to the colonization of the gut microbiota in pigs remains unclear. Here, we longitudinally sampled the microbiota of 20 sow-piglet pairs (three piglets per sow) reared under identical conditions from multiple body sites and the surrounding weaning environment from birth to 28 days postpartum (1,119 samples in total). Source-tracking analysis revealed that the contribution of various microbial sources to the piglet gut microbiome gradually changed over time. The neonatal microbiota was initially sparsely populated, and the predominant contribution was from the maternal vaginal microbiota that increased gradually from 69.0% at day 0 to 89.3% at day 3 and dropped to 0.28% at day 28. As the piglets aged, the major microbial community patterns were most strongly associated with the sow feces and slatted floor, with contributions increasing from 0.52 and 9.6% at day 0 to 62.1 and 33.8% at day 28, respectively. The intestinal microbial diversity, composition, and function significantly changed as the piglets aged, and 30 age-discriminatory bacterial taxa were identified with distinctive time-dependent shifts in their relative abundance, which likely reflected the effect of the maternal and environmental microbial sources on the selection and adaptation of the piglet gut microbiota. Overall, these data demonstrate that the vaginal microbiota is the primary source of the gut microbiota in piglets within 3 days after birth and are gradually replaced by the sow fecal and slatted floor microbiota over time. These findings may offer novel strategies to promote the establishment of exogenous symbiotic microbes to improve piglet gut health.

Metagenome-Assembled Genomes Reveal Mechanisms of Carbohydrate and Nitrogen Metabolism of Schistosomiasis-Transmitting Vector Biomphalaria Glabrata

Biomphalaria glabrata transmits schistosomiasis mansoni which poses considerable risks to hundreds of thousands of people worldwide, and is widely used as a model organism for studies on the snail-schistosome relationship. Gut microbiota plays important roles in multiple aspects of host including development, metabolism, immunity, and even behavior; however, detailed information on the complete diversity and functional profiles of B. glabrata gut microbiota is still limited. This study is the first to reveal the gut microbiome of B. glabrata based on metagenome-assembled genome (MAG). A total of 28 gut samples spanning diet and age were sequenced and 84 individual microbial genomes with ≥ 70% completeness and ≤ 5% contamination were constructed. Bacteroidota and Proteobacteria were the dominant bacteria in the freshwater snail, unlike terrestrial organisms harboring many species of Firmicutes and Bacteroidota. The microbial consortia in B. glabrata helped in the digestion of complex polysaccharide such as starch, hemicellulose, and chitin for energy supply, and protected the snail from food poisoning and nitrate toxicity. Both microbial community and metabolism of B. glabrata were significantly altered by diet. The polysaccharide-degrading bacterium Chryseobacterium was enriched in the gut of snails fed with high-digestibility protein and high polysaccharide diet (HPHP). Notably, B. glabrata as a mobile repository can escalate biosafety issues regarding transmission of various pathogens such as Acinetobacter nosocomialis and Vibrio parahaemolyticus as well as multiple antibiotic resistance genes in the environment and to other organisms. IMPORTANCE The spread of aquatic gastropod Biomphalaria glabrata, an intermediate host of Schistosoma mansoni, exacerbates the burden of schistosomiasis disease worldwide. This study provides insights into the importance of microbiome for basic biological activities of freshwater snails, and offers a valuable microbial genome resource to fill the gap in the analysis of the snail-microbiota-parasite relationship. The results of this study clarified the reasons for the high adaptability of B. glabrata to diverse environments, and further illustrated the role of B. glabrata in accumulation of antibiotic resistance in the environment and spread of various pathogens. These findings have important implications for further exploration of the control of snail dissemination and schistosomiasis from a microbial perspective.

Gut Bacterial Composition and Functional Potential of Tibetan Pigs Under Semi-Grazing

Gut bacterial community plays a key role in maintaining host health. The Tibetan pig (Sus scrofa), an ancient breed in China, has been known for its high adaptability to harsh environments and for its meat quality. To understand the underlying mechanisms facilitating to shape these unique features, in this study, 16S rRNA sequencing using pigs feces and subsequent bacterial functional prediction were performed. Also, the gut bacteria of two other breeds of pigs, Barkshire and Landrace, were examined for comparison. It was revealed that the structure of bacterial community in Tibetan pigs appeared to be more complex; the relative abundances of dominant bacterial families varied inversely with those of the other pigs, and the proportion of Firmicutes in Tibetan pigs was lower, but Bacteroides, Fibrobacterota, Lachnospiraceae, Oscillospiraceae, and Ruminococcaceae were higher. Bacterial functional prediction revealed that the dominant flora in the Tibetan pigs was more correlated with functions regulating the hosts’ immune and inflammatory responses, such as NOD-like_receptor_signaling_pathway and vitamin metabolism. In addition, in Tibetan pigs, the taxonomic relationships in the gut bacteria on day 350 were closer than those on earlier stages. Furthermore, gender played a role in the composition and function of bacterial inhabitants in the gut; for boars, they were more correlated to drug resistance and xenobiotics metabolism of the host compared to the sows. In sum, our preliminary study on the gut bacterial composition of the Tibetan pigs provided an insight into the underlying host–microorganism interactions, emphasizing the role of intestinal bacteria in the context of modulating the host’s immune system and host development.

Microbial Biogeography along the Gastrointestinal Tract Segments of Sympatric Subterranean Rodents (Eospalax baileyi and Eospalax cansus)

Simple Summary

The gut microbiota are crucial for hosts. For mammals, different gastrointestinal tract (GIT) segments have specific microbial communities, which play an essential role in the host’s nutrition, metabolism, immunity, and health. Plateau zokors (Eospalax baileyi) and Gansu zokors (Eospalax cansus) are closely related species that belong to the Spalacidae family, and are common pests in agriculture, forestry, and animal husbandry in northwestern China, with a sympatric distribution area in the transition zone between the Qinghai-Tibetan Plateau and the Loess Plateau. Here, the characteristics of the microbiota communities in different GIT segments of the plateau zokor and the Gansu zokor were studied, and the microbiota communities of the two zokor species were compared. Our results provide important information for further study on the function of microbiota communities in different GIT segments and the potential use of the gut microbiota as a new method for the population management of the zokors.

Abstract

In this study, based on high-throughput sequencing technology, the biodiversity and the community structure of microbiota in different GIT segments (the stomach, small intestine, cecum and rectum) of plateau zokors and Gansu zokors were studied and compared. A source tracking analysis for the microbial communities of different GIT segments was carried out using the fast expectation–maximization microbial source tracking (FEAST) method. We found that, for both species, the microbial community richness and diversity of the small intestine were almost the lowest while those of the cecum were the highest among the four segments of the GIT. Beta diversity analyses revealed that the bacterial community structures of different GIT segments were significantly different. As for the comparison between species, the bacterial community compositions of the whole GIT, as well as for each segment, were all significantly different. Source tracking conducted on both zokors indicated that the soil has little effect on the bacterial community of the GIT. A fairly high percentage of rectum source for the bacterial community of the stomach indicated that both zokors may engage in coprophagy.