De novo semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data

Gut microbiota in the association between obesity and kidney function decline: a metagenomics-based study in a rat model

OBJECTIVES

Obesity can induce dysbiosis in the gut microbiota and is considered a separate risk factor for kidney function decline. Nonetheless, the precise function of intestinal microorganisms in facilitating the connection between obesity and kidney function decline remains uncertain. Hence, the objective of this study was to investigate the alterations in the gut microbiota composition that take place during obesity and their correlations with renal function utilizing a rat model.

METHODS

For 20 weeks, 25 Sprague-Dawley rats were fed either a high-fat diet (HFD) or a normal-fat normal diet (ND). Physiological indices, peripheral plasma, kidney tissue, and colon contents were collected for comparison between groups. Metagenomic analysis of intestinal flora was performed.

RESULTS

The HFD group demonstrated significantly increased levels of creatinine and urea nitrogen in the peripheral blood. Additionally, the HFD rats exhibited a significantly larger glomerular diameter compared to the ND group, accompanied by the presence of glomerulosclerosis, tubular vacuolar transformation, and other pathological changes in certain glomeruli. Metagenomics analysis revealed a notable rise in the prevalence of the Firmicutes phylum within the HFD group, primarily comprising the Rumenococcus genus. Functional analysis indicated that the gut microbiota in the HFD group primarily correlated with infectious diseases, signal transduction, and signaling molecules and interactions.

CONCLUSIONS

This study provides evidence that the consumption of a HFD induces modifications in the composition and functionality of the gut microbiome in rats, which may serve as a potential mechanism underlying the relationship between obesity and the progression of kidney function decline.

Exploring microbial diversity and function in companion planting systems of white clover and orchard grass

Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.

Intestinal microbiota dataset revealed by high-throughput sequencing of 16S rRNA in children with anemia in southern Peru

Anemia is the most common hematological disorder affecting humans. In Peru, anemia is a pressing issue that present the most significant concern due to its adverse effects, such as delayed growth and psychomotor development, in addition to a deficiency in cognitive development. Anemia is a significant public health issue in Peru, which has one of the highest prevalence rates in infants in the Latin American and Caribbean (LAC) region, affecting approximately 43.6 % of children under three years nationally as of 2017, with rural areas experiencing a higher prevalence of approximately 53.3 %. In 2019, the prevalence was highest in the Sierra (48.8 %) and Selva regions (44.6 %), whereas the coast had a lower rate of 33.9 % in children under 36 months. Although the composition of the gut microbiota is relatively well described in children, there is little information on the identification of the microbiota in iron-deficiency anemia. There is evidence that diseases or health conditions can change the microbiota, or vice versa. This study aimed to identify the microbiota in children with anemia who did not recover after iron treatment. In a previous study, we found that the phylum Actinobacteria was predominant in the microbiota of children with anemia. These data will be useful for understanding the functionality of the most important bacteria found in each group at the genus or species level, especially the metabolic pathways in which they participate and their links with iron metabolism. Microbial composition data were obtained through next-generation 16S rRNA sequencing (NGS) of stool samples from children with anemia in southern Peru. Numerous studies have underscored the importance of early symbiotic development in infant health and its long-term impact on health. From infancy, modulation of the gut microbiota can promote long-term health. According to the National Institute of Health (NIH), iron-deficiency anemia may cause serious complications, such as fatigue, headaches, restless legs syndrome, heart problems, pregnancy complications, and developmental delays in children. The development of the gut microbiota is regulated by a complex interplay between host and environmental factors. The bidirectional link between the gut microbiota and anemia plays an important role in tracking the gut microbiota and will be useful in understanding the composition of the intestinal microbiota and its implications in anemia, which has now become a public health problem. Our previous study investigated the microbial composition in children with iron-deficiency anemia and revealed the presence of several bacterial groups, including Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi. In addition, these data may be useful for investigating the association between the intestinal microbiota of children with persistent anemia and those who have recovered.

Breaking the Cycle: A Yeast Mannan-Rich Fraction Beneficially Modulates Egg Quality and the Antimicrobial Resistome Associated with Layer Hen Caecal Microbiomes under Commercial Conditions

Antibiotics and antibiotic growth promoters have been extensively employed in poultry farming to enhance growth performance, maintain bird health, improve nutrient uptake efficiency, and mitigate enteric diseases at both sub-therapeutic and therapeutic doses. However, the extensive use of antimicrobials in poultry farming has led to the emergence of antimicrobial resistance (AMR) in microbial reservoirs, representing a significant global public health concern. In response, non-antibiotic dietary interventions, such as yeast mannan-rich fraction (MRF), have emerged as a promising alternative to modulate the gut microbiota and combat the AMR crisis. This study investigated whether a yeast mannan-rich fraction containing feed supplement impacted the performance of laying hens, their microbiomes, and the associated carriage of antimicrobial resistance genes under commercial conditions. High-throughput DNA sequencing was utilised to profile the bacterial community and assess changes in the antibiotic resistance genomes detected in the metagenome, the "resistome", in response to MRF supplementation. It was found that supplementation favourably influenced laying hen performance and microbial composition. Notably, there was a compositional shift in the MRF supplemented group associated with a lower relative abundance of pathobionts, e.g., Escherichia, Brachyspira and Trueperella, and their AMR-encoded genes, relative to beneficial microbes. Overall, the findings further demonstrate the ability of prebiotics to improve laying hen performance through changes associated with their microbiome and resistome.

Lactobacillus rhamnosus 069 and Lactobacillus brevis 031: Unraveling Strain-Specific Pathways for Modulating Lipid Metabolism and Attenuating High-Fat-Diet-Induced Obesity in Mice

Obesity is a global health crisis, marked by excessive fat in tissues that function as immune organs, linked to microbiota dysregulation and adipose inflammation. Investigating the effects of Lactobacillus rhamnosus SG069 (LR069) and Lactobacillus brevis SG031 (LB031) on obesity and lipid metabolism, this research highlights adipose tissue's critical immune-metabolic role and the probiotics' potential against diet-induced obesity. Mice fed a high-fat diet were treated with either LR069 or LB031 for 12 weeks. Administration of LB031 boosted lipid metabolism, indicated by higher AMP-activated protein kinase (AMPK) and acetyl-CoA carboxylase (ACC) phosphorylation, and increased the M2/M1 macrophage ratio, indicating LB031's anti-inflammatory effect. Meanwhile, LR069 administration not only led to significant weight loss by enhancing lipolysis which evidenced by increased phosphorylation of hormone-sensitive lipase (HSL) and adipose triglyceride lipase (ATGL) but also elevated Akkermansia and fecal acetic acid levels, showing the gut microbiota's pivotal role in its antiobesity effects. LR069 and LB031 exhibit distinct effects on lipid metabolism and obesity, underscoring their potential for precise interventions. This research elucidates the unique impacts of these strains on metabolic health and highlights the intricate relationship between gut microbiota and obesity, advancing our knowledge of probiotics' therapeutic potential.

Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems

Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.

Very low-carbohydrate diet with higher protein ratio improves lipid metabolism and inflammation in rats with diet-induced nonalcoholic fatty liver disease

Non-alcoholic fatty liver disease (NAFLD) is commonly associated with obesity, and it is mainly treated through lifestyle modifications. The very low-carbohydrate diet (VLCD) can help lose weight rapidly but the possible effects of extreme dietary patterns on lipid metabolism and inflammatory responses in individuals with NAFLD remain debatable. Moreover, VLCD protein content may affect its effectiveness in weight loss, steatosis, and inflammatory responses. Therefore, we investigated the effects of VLCDs with different protein contents in NAFLD rats and the mechanisms underlying these effects. After a 16-week inducing period, the rats received an isocaloric normal diet (NC group) or a VLCD with high or low protein content (NVLH vs. NVLL group, energy ratio:protein/carbohydrate/lipid=20/1/79 vs. 6/1/93) for the next 8 weeks experimental period. We noted that the body weight decreased in both the NVLH and NVLL groups; nevertheless, the NVLH group demonstrated improvements in ketosis. The NVLL group led to hepatic lipid accumulation, possibly by increasing very-low-density lipoprotein receptor (VLDLR) expression and elevating liver oxidative stress, subsequently activating the expression of Nrf2, and inflammation through the TLR4/TRIF/NLRP3 and TLR4/MyD88/NF-κB pathway. The NVLH was noted to prevent the changes in VLDLR and the TLR4-inflammasome pathway partially. The VLCD also reduced the diversity of gut microbiota and changed their composition. In conclusion, although low-protein VLCD consumption reduces BW, it may also lead to metabolic disorders and changes in microbiota composition; nevertheless, a VLCD with high protein content may partially alleviate these limitations.

A New 4-Thiazolidinone Derivative (Les-6490) as a Gut Microbiota Modulator: Antimicrobial and Prebiotic Perspectives

A novel 4-thiazolidinone derivative Les-6490 (pyrazol-4-thiazolidinone hybrid) was designed, synthesized, and characterized by spectral data. The compound was screened for its antimicrobial activity against some pathogenic bacteria and fungi and showed activity against Staphylococcus and Saccharomyces cerevisiae (the Minimum Inhibitory Concentration (MIC) 820 μM). The compound was studied in the rat adjuvant arthritis model (Freund's Adjuvant) in vivo. Parietal and fecal microbial composition using 16S rRNA metagenome sequences was checked. We employed a range of analytical techniques, including Taxonomic Profiling (Taxa Analysis), Diversity Metrics (Alpha and Beta Diversity Analysis), Multivariate Statistical Methods (Principal Coordinates Analysis, Principal Component Analysis, Non-Metric Multidimensional Scaling), Clustering Analysis (Unweighted Pair-group Method with Arithmetic Mean), and Comparative Statistical Approaches (Community Differences Analysis, Between Group Variation Analysis, Metastat Analysis). The compound significantly impacted an increasing level of anti-inflammatory microorganisms (Blautia, Faecalibacterium prausnitzii, Succivibrionaceae, and Coriobacteriales) relative recovery of fecal microbiota composition. Anti-Treponemal activity in vivo was also noted. The tested compound Les-6490 has potential prebiotic activity with an indirect anti-inflammatory effect.

Influence of pancreaticoduodenectomy for periampullary carcinoma on intestinal microbiome and metabolites

Recent growing evidence suggests a role for intestinal microbiome and metabolites in patients' postoperative recovery. Therefore, there is a need to gain insight into the impact of pancreaticoduodenectomy for periampullary carcinoma on microbiome and metabolites and the potential impact of their changes on patients' condition. Based on 16S rDNA gene sequencing and untargeted metabolomic analysis, we found that the diversity and abundance of intestinal microbiome were significantly higher in patients preoperatively than postoperatively, and the level of intestinal probiotics was significantly lower after surgery compared with preoperatively. In addition, the choline metabolism level was increased and the amino acid metabolism level was decreased after surgery. A total of 53 differential microbiome and 52 differential metabolites were detected, and the differential metabolites were mapped to approximately 60 different KEGG metabolic pathways, of which 13 KEGG metabolic pathways had a differential metabolite number greater than 5. A total of 88 colony-metabolite pairs with significant positive correlation and 69 colony-metabolite pairs with significant negative correlation were identified. Our results reveal alterations in intestinal microbiome after pancreaticoduodenectomy, suggesting its association with postoperative complications. Moreover, the elevated choline metabolism level in postoperative patients may predict their poorer prognosis. At the same time, the decreased abundance of such probiotic bacteria as Prevotella spp. in the postoperative intestine of patients will affect the amino acid metabolism of the organism to some extent.

Effects of Vitamin A on Growth Performance, Antioxidants, Gut Inflammation, and Microbes in Weaned Piglets

Piglet weaning is an important stage in production where changes in the environment and diet can cause problems such as intestinal inflammation and diarrhea. Vitamin A is an essential nutrient for human and animal growth and has immunomodulatory and inflammatory effects. A large body of literature has previously reported on the use of vitamin A in piglet production, so our experiment added different concentrations of vitamin A (0, 1100, 2200, 4400, 8800, and 17,600 IU/kg) to weaned piglet diets to study the effects of different doses on growth performance, intestinal barrier, inflammation, and flora in weaned piglets. We selected 4400 IU/kg as the optimum concentration of vitamin A in relation to average daily weight gain, feed intake, feed-to-weight ratio, and diarrhea rate, and subsequently tested the inflammatory factors, immunoglobulin content, antioxidant levels, and intestinal flora of weaned piglets. Results: We observed that the diarrhea rate of weaned piglets was significantly lower after the addition of 4400 IU/kg of vitamin A to the diet (p < 0.05). A control group and a 4400 IU/kg VA group were selected for subsequent experiments. We found that after the addition of vitamin A, the serum CAT level of weaned piglets increased significantly, the expression of Claudin-1 in the jejunum and ileum increased significantly, the expression of Occludin gene in the jejunum increased significantly, the expression of IL-5 and IL-10 in the ileum increased significantly (p < 0.05), and the expression of IL-4, IL-5, and IL-10 in the ileum increased significantly (p < 0.05). Meanwhile, in the colonic flora of vitamin A-added weaned piglets, the relative abundance of Actinobacteria and Erysipelotrichales decreased significantly, while the relative abundance of Bacteroidales increased significantly (p < 0.05). The results of this study indicated that vitamin A at 4400 IU/kg reduces diarrhea in weaned piglets by increasing antioxidant levels, increasing intestinal tight junction protein gene expression, and regulating colonic gut microbiota.

Partial Replacement of Diet with Dehulled Adlay Ameliorates Hepatic Steatosis, Inflammation, Oxidative Stress, and Gut Dysbiosis in Rats with Nonalcoholic Fatty Liver Disease

The prevalence of nonalcoholic fatty liver disease (NAFLD) has been increasing worldwide, and the average age at NAFLD diagnosis has been decreasing. Although some components of adlay can ameliorate lipid metabolism, oxidative stress, inflammatory response, and gut microbiota, few studies have explored the effects of the dietary intake of intact dehulled adlay on liver diseases. Therefore, in this study, we investigated the effects of the dietary intake of dehulled adlay on NAFLD progression and explored the potential underlying mechanisms. Rats were randomized into a control group; a high-fat, high-sucrose diet (60% total energy derived from fat and 9.4% from sucrose)-induced NAFLD group (N); or a high-fat, high-sucrose diet with dehulled adlay group (received the same amounts of dietary fiber and total energy as did the N group). The experimental duration was 16 weeks. The diet containing dehulled adlay mitigated hepatic fat accumulation, proinflammatory cytokine levels, and oxidative stress by regulating the AMPK-Nrf2-NLRP3 inflammasome pathway and ferroptosis. Additionally, the dietary intake of dehulled adlay modulated the composition of the gut microbiota. In conclusion, a diet containing dehulled adlay may decelerate the progression of NAFLD by ameliorating hepatic steatosis, inflammation, oxidative stress, and gut dysbiosis.

A Preliminary Study of the Potential Molecular Mechanisms of Individual Growth and Rumen Development in Calves with Different Feeding Patterns

At present, it is common to feed calves with "Concentrate", "Concentrate + hay" and TMR "Total Mixed Rations" feeding patterns in China, which achieved well feeding efficiency, but the three feeding patterns molecular regulation mechanism in actual production is still unclear. The study aimed to explore the most suitable feeding pattern for Chinese Holstein calves to improve the rumen fermentation function and growth performance of calves. In this regard, the interactions between rumen microorganisms and host metabolism were investigated. The rumen volume and weight of calves in the GF group were significantly higher than those in the GFF and TMR groups (p < 0.05), and the rumen pH of calves in the GF group was 6.47~6.79. Metagenomics analysis revealed that the rumen microbiome of GF and GFF calves had higher relative abundances of Methanobrevibacter, Methanosphaera, and Methanolacinia (p < 0.05). Prevotella multisaccharivorax was significantly more abundant in the rumen of GF calves (p < 0.05), indicating that GF group calves had a stronger ability to ferment sugars. Notably, in the pyruvate metabolic pathway, phosphoenolpyruvate carboxylase was significantly up-regulated in GF calves compared with the TMR group, and pyruvate-phosphate dikinase was significantly down-regulated. Metabolomic results showed that Ursodeoxycholic acid was significantly up-regulated in GF calves, and most of the differential metabolites were enriched in Bile secretion pathways. The association analysis study found that the microorganisms of Prevotella and Ruminococcaceae might cooperate with the host, which was helpful for the digestion and absorption of lipids and made the calves have better growth. The three feeding modes had similar effects, but the 'GF' feeding pattern was more beneficial to the individual growth and ruminal development regarding ruminal morphology, contents physiology and microorganisms. Furthermore, the synergistic effect of rumen microorganisms and the host could more effectively hydrolyze lipid substances and promote the absorption of lipids, which was of great significance to the growth of calves.

Metagenomic Analysis Reveals Variations in Gut Microbiomes of the Schistosoma mansoni-Transmitting Snails Biomphalaria straminea and Biomphalaria glabrata

Biomphalaria snails play a crucial role in the transmission of the human blood fluke Schistosoma mansoni. The gut microbiota of intermediate hosts is known to influence their physiological functions, but little is known about its composition and role in Biomphalaria snails. To gain insights into the biological characteristics of these freshwater intermediate hosts, we conducted metagenomic sequencing on Biomphalaria straminea and B. glabrata to investigate variations in their gut microbiota. This study revealed that the dominant members of the gut microbiota in B. glabrata belong to the phyla Bacteroidetes and Proteobacteria, which were also found to be the top two most abundant gut bacteria in B. straminea. We identified Firmicutes, Acidovorax and Bosea as distinctive gut microbes in B. straminea, while Aeromonas, Cloacibacterium and Chryseobacterium were found to be dependent features of the B. glabrata gut microbiota. We observed significant differences in the community structures and bacterial functions of the gut microbiota between the two host species. Notably, we found a distinctive richness of antibiotic resistance genes (ARGs) associated with various classes of antibiotics, including bacitracin, chloramphenicol, tetracycline, sulfonamide, penicillin, cephalosporin_ii and cephalosporin_i, fluoroquinolone, aminoglycoside, beta-lactam, multidrug and trimethoprim, in the digestive tracts of the snails. Furthermore, this study revealed the potential correlations between snail gut microbiota and the infection rate of S. mansoni using Spearman correlation analysis. Through metagenomic analysis, our study provided new insights into the gut microbiota of Biomphalaria snails and how it is influenced by host species, thereby enhancing our understanding of variant patterns of gut microbial communities in intermediate hosts. Our findings may contribute to future studies on gastropod-microbe interactions and may provide valuable knowledge for developing snail control strategies to combat schistosomiasis in the future.

Unravelling Metabolic Heterogeneity of Chinese Baijiu Fermentation in Age-Gradient Vessels

Fermentation vessels affect the characteristics of food fermentation; however, we lack an approach to identify the biomarkers indicating fermentation. In this study, we applied metabolomics and high-throughput sequencing analysis to reveal the dynamic of metabolites and microbial communities in age-gradient fermentation vessels for baijiu production. Furthermore, we identified 64 metabolites during fermentation, and 19 metabolites significantly varied among the three vessels (p < 0.05). Moreover, the formation of these 19 metabolites were positively correlated with the core microbiota (including Aspergillus, Saccharomyces, Lactobacillus, and Bacillus). In addition, ethyl lactate or ethyl acetate were identified as the biomarkers for indicating the metabolism among age-gradient fermentation vessels by BP-ANN (R2 > 0.40). Therefore, this study combined the biological analysis and predictive model to identify the biomarkers indicating metabolism in different fermentation vessels, and it also provides a potential approach to assess the profiling of food fermentations.

The effects of differential feeding on ileum development, digestive ability and health status of newborn calves

Pre-weaning is the most important period for the growth and development of calves. Intestinal morphology, microbial community and immunity are initially constructed at this stage, and even have a lifelong impact on calves. Early feeding patterns have a significant impact on gastrointestinal development and microbial communities. This study mainly analyzed the effects of three feeding methods on the gastrointestinal development of calves, and provided a theoretical basis for further improving the feeding mode of calves. it is very important to develop a suitable feeding mode. In this study, we selected nine newborn healthy Holstein bull calves were randomly selected and divided into three groups (n = 3), which were fed with starter + hay + milk (SH group), starter + milk (SF group), total mixed ration + milk (TMR group). After 80 days of feeding Feeding to 80 days of age after, the ileum contents and blood samples were collected, and the differences were compared and analyzed by metagenomic analysis and serum metabolomics analysis. Results show that compared with the other two groups, the intestinal epithelium of the SH group was more complete and the goblet cells developed better. The feeding method of SH group was more conducive to the development of calves, with higher daily gain and no pathological inflammatory reaction. The intestinal microbial community was more conducive to digestion and absorption, and the immunity was stronger. These findings are helpful for us to explore better calf feeding patterns. In the next step, we will set up more biological replicates to study the deep-seated reasons for the differences in the development of pre-weaning calves. At the same time, the new discoveries of neuro microbiology broaden our horizons and are the focus of our future attention.

Intestinal acetic acid regulates the synthesis of sex pheromones in captive giant pandas

As a typical solitary animal, adult giant pandas rely on chemical signals (sex pheromones) to transmit reproductive information during oestrous. Although researchers have confirmed that the gut microbiota is related to the emission and reception of sex pheromones, there is no clear correlation between the gut microbes and the synthesis of sex pheromone of giant pandas, that is, which gut microbes and microbial metabolites are participate in the synthesis of giant panda's sex pheromone. As a mirror of gut microbiota, fecal microbiota can reflect the composition of gut microbiota and its interaction with host to some extent. The purpose of this study is to explore how the gut microbes affect the synthesis of sex pheromones in captive giant pandas by combining analysis of the fecal microbiome and metabolomics. The results of correlation and microbial function analysis show that intestinal microorganisms such as Veillonellaceae and Lactobacillilaceae are associated with the synthesis of short chain fatty acid (acetic acid) and volatile ester metabolites, such as 1-butanol, 3-methyl, acetate, acetic acid, hexyl ester and 3-hexen-1-ol, acetate, (Z). In summary, based on this study, we believe that volatile metabolites such as fecal acetate participate in the process of mate preference of captive giant pandas and affect their expression of natural mating behavior. The possible mechanism is that the gut microbes can promote the synthesis of key chemical signaling substances in perianal glands through mediated intermediate fecal metabolites, thus affecting the normal information exchange between giant pandas individuals. The results of this study have greatly enriched our understanding of gut microbes regulating the synthesis of sex pheromones in giant pandas.

Effects of Candidatus Liberibacter asiaticus infection on metagenome of Diaphorina citri gut endosymbiont

Asian citrus psyllid (Diaphorina citri, D. citri) is the important vector of "Candidatus Liberibacter asiaticus" (CLas), associated with Huanglongbing, the most devastating citrus disease worldwide. CLas can affect endosymbiont abundance of D. citri. Here, we generated the high-quality gut endosymbiont metagenomes of Diaphorina citri on the condition of CLas infected and uninfected. The dataset comprised 6616.74 M and 6586.04 M raw reads, on overage, from CLas uninfected and infected psyllid strains, respectively. Taxonomic analysis revealed that a total of 1046 species were annotated with 10 Archaea, 733 Bacteria, 234 Eukaryota, and 69 Viruses. 80 unique genera in CLas infected D. citri were identified. DIAMOND software was used for complement function research against various functional databases, including Nr, KEGG, eggNOG, and CAZy, which annotated 84543 protein-coding genes. These datasets provided an avenue for further study of the interaction mechanism between CLas and D. citri.

Comparative Functional Genome Analysis Reveals the Habitat Adaptation and Biocontrol Characteristics of Plant Growth-Promoting Bacteria in NCBI Databases

Plant growth-promoting bacteria (PGPB) are a group of beneficial microorganisms that include 60 bacterial genera, such as Bacillus, Pseudomonas, and Burkholderia, which widely colonize plant leaves and soil, promote plant growth, and/or inhibit pathogen infection. However, the genetic factors underpinning adaptation of PGPB to plant leaves and soil remain poorly understood. In this study, we performed a comparative functional genome analysis approach to investigate the functional genes of 195 leaf-associated (LA) and 283 soil-associated (SA) PGPB strains and their roles in adapting to their environment, using 95 strains from other-associated (OA) environmental habitats with growth-promoting or antimicrobial functions as negative controls. Comparison analysis of the enrichment of nonredundant (NR) protein sequence databases showed that cytochrome P450, DNA repair, and motor chemotaxis genes were significantly enriched in LA PGPB strains related to environmental adaptation, while cell wall-degrading enzymes, TetR transcriptional regulatory factors, and sporulation-related genes were highly enriched in SA PGPB strains. Additionally, analysis of carbohydrate-active enzymes demonstrated that glycosyltransferases (GTs) and glycoside hydrolases (GHs) were abundant families in all PGPB strains, which is in favor of plant growth, and enriched in SA PGPB strains. Except for most Bacillus strains, SA PGPB genomes contained significantly more secondary metabolism clusters than LA PGPB. Most LA PGPB contained hormone biosynthesis genes, which may contribute to plant growth promotion, while SA PGPB harbored numerous carbohydrate and antibiotic metabolism genes. In summary, this study further deepens our understanding of the habitat adaptation and biocontrol characteristics of LA and SA PGPB strains. IMPORTANCE Plant growth-promoting bacteria (PGPB) are essential for the effectiveness of biocontrol agents in plant phyllosphere and rhizosphere. However, little is known about the ecological adaptation of PGPB to different habitats. In this study, comparative functional genome analysis of leaf-associated (LA), soil-associated (SA), and other-associated (OA) PGPB strains was performed. We found that genes related to the metabolism of hormones were enriched in LA PGPB. Carbohydrate and antibiotic metabolism genes were enriched in SA PGPB, which likely facilitated their adaptation to the plant growth environment. Our findings provide genetic insights on LA and SA PGPB strains' ecological adaptation and biocontrol characteristics.

Maternal Vitamin A deficiency during pregnancy and lactation induced damaged intestinal structure and intestinal flora homeostasis in offspring mice

The small intestine serves as the first channel of dietary Vitamin A (VA) and the unique organ of VA absorption and metabolism. However, there have not been extensive investigations on the exact mechanisms within VA-related changes in intestinal metabolic disorders. This research is designed to analyze whether and how VA affects intestinal metabolic phenotypes. Male C57BL/6 mice after weaning were randomly fed a VA control diet (VAC) or a VA-deficient diet (VAD) during the entire pregnancy and lactation process. After a total of 11 weeks, cohorts of VA deprived were next fed to a VA control diet (VAD-C) for another 8 weeks. The concentration of retinol was measured by a high-performance liquid chromatography system. The 16S gene sequencing was used to evaluate the intestinal microbiota changes. Through the use of histological staining, western blots, quantitative PCR, and enzyme-linked immunosorbent assays, the intestinal morphology, inflammatory factors, and intestinal permeability were all evaluated. Following the decrease of the tissue VA levels, VAD mice show a decrease in tissue VA levels, community differences, and the richness and diversity of intestinal microbiota. VAD diet-driven changes occur in intestinal microbiota, accompanied by a higher mRNA expression of intestinal inflammatory cytokines and an increase in intestinal permeability. As dietary VA is reintroduced into VAD diet-fed mice, the tissue VA levels, inflammatory response, and intestinal homeostasis profiles are all restored, which are similar to those found after the occurrence of VA-controlled changes within intestinal microbiota. VA deficiency caused the imbalance of intestinal metabolic phenotypes through a mechanism involving changes in intestinal microbiota. It is thought that intestinal microbiota metabolic influences represent a new salient and additional mechanism, which can be used as a new method to achieve the onset and treatment of the effect of VAD on intestinal homeostasis impairment.

Effects of levodopa on gut bacterial antibiotic resistance in Parkinson's disease rat

The second most prevalent neurodegenerative ailment, Parkinson's disease (PD), is characterized by both motor and non-motor symptoms. Levodopa is the backbone of treatment for PD at the moment. However, levodopa-induced side effects, such as dyskinesia, are commonly seen in PD patients. Recently, several antibiotics were found to present neuroprotective properties against neurodegenerative and neuro-inflammatory processes, which might be developed to effective therapies against PD. In this study, we aimed to identify if levodopa treatment could influence the gut bacterial antibiotic resistance in PD rat. Fecal samples were collected from healthy rats and 6-OHDA induced PD rats treated with different doses of levodopa, metagenomic sequencing data showed that levodopa resulted in gut bacteria composition change, the biomarkers of gut bacteria analyzed by LEfSe changed as well. More interestingly, compared with levodopa (5 mg/kg)-treated or no levodopa-treated PD rats, levodopa (10 mg/kg) caused a significant decrease in the abundance of tetW and vanTG genes in intestinal bacteria, which were related to tetracycline and vancomycin resistance, while the abundance of AAC6-lb-Suzhou gene increased apparently, which was related to aminoglycosides resistance, even though the total quantity of Antibiotic Resistance Gene (ARG) and Antibiotic Resistance Ontology (ARO) among all groups did not significantly differ. Consequently, our results imply that the combination of levodopa and antibiotics, such as tetracycline and vancomycin, in the treatment of PD may decrease the amount of corresponding antibiotic resistance genes in gut bacteria, which would give a theoretical basis for treating PD with levodopa combined with tetracycline and vancomycin in the future.

A new potential risk: The impacts of Klebsiella pneumoniae infection on the histopathology, transcriptome and metagenome of Chinese mitten crab (Eriocheir sinensis)

Klebsiella pneumoniae is a common conditional pathogen found in natural soil water sources and vegetation and can infect invertebrates, vertebrates, and plants. In this study, we isolated K. pneumoniae from the hepatopancreas of the Chinese mitten crab (Eriocheir sinensis) for the first time and then we analysed its effects of on the histopathological changes, the transcriptome of the hepatopancreas, and the gut microbiota of this crab species. The findings of this study showed that K. pneumoniae infection has led to significant structural changes in the hepatopancreas, such as the production of vacuolated tissue structures, disorganized cell arrangement, and lysis of some hepatopancreatic cells. Also, the infection caused activation of the antioxidant-related enzymes such as SOD and CAT by inducing oxidative stress. The transcriptome of the hepatopancreas identified 10,940 differentially expressed genes (DEGs) in the susceptible (SG) groups and control (CG) groups, and 8495 DEGs in the SG groups and anti-infective (AI) groups. The KEGG pathway revealed upregulated DEGs caused by K. pneumoniae infection that involved in the immune response and apoptotic functional pathways, and also downregulated DEGs involved in the digestive absorption, metabolic, and biosynthetic signaling pathways. Meanwhile, metagenics sequencing revealed that at the phylum, class, order, family, and genus levels, K. pneumoniae infection altered the composition of the gut microbiota of E. sinensis, through increasing the abundance of Prolixibacteraceae, Enterobacterales, and Roseimarinus and decreasing the abundance of Alphaproteobacteria. The flora structure has also been changed between the SG and AI groups, with the abundance of Firmicutes, Erysipelotrichales, and Erysipelotrichaceae that were significantly decreased in the SG groups than in the AI groups. But, the abundance of Acinetobacter was considerably higher than in the AI group. In summary, K. pneumoniae infection induced oxidative stress in E. sinensis, triggered changes in immune-related gene expression, and caused structural changes in the gut microbiota. This study provides data to support the analysis of bacterial infection probes in several crustacean species.

Bacillus velezensis Strain GUMT319 Reshapes Soil Microbiome Biodiversity and Increases Grape Yields

Bacillus velezensis strain GUMT319 is a rhizobacteria biocontrol agent that can control tobacco black shank disease. We took GUMT319 as a biological fertilizer on Vitis vinifera L. The test group was treated with GUMT319 for one year and the control group had a water treatment. Yields of GUMT319-treated grape groups were significantly increased compared to the controls. The average length and width of single grape fruit, weight of 100 grape fruits, the sugar/acid ratio, and the content of vitamin C were all increased in the GUMT319-treated grape group. The pH of the soil was higher and the contents of alkaline hydrolyzable nitrogen and available potassium were significantly lower in the GUMT319-treated groups than the controls. The soil microbial community composition was evaluated by 16S rDNA high-throughput sequencing, and the Shannon index and Simpson index all showed that soil microbes were more abundant in the GUMT319-treated group. These results indicate that GUMT319 is not only a biocontrol agent, but also a plant growth-promoting rihizobacteria. It can increase the yield of grape by altering the physical and chemical properties and the microbial community composition of the soil.

Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken

Coccidiosis is an economically significant protozoan disease and an intracellular parasite that significantly impacts poultry production. The gastrointestinal tract microbiota plays a central role in host health and metabolism, and these microbes enhance chickens’ immune systems and nutrient absorption. In this study, we analyzed the abundance and diversity of microbiota of the jejunum and cecum of a dual-purpose indigenous Horro chicken following Eimeria maxima infection. We compared microbial abundance, composition, and diversity at the 4- and 7- days post-infection using 16S rRNA gene sequencing. We obtained, on average, 147,742 and 132,986 high-quality sequences per sample for jejunum and cecum content, respectively. Firmicutes, Proteobacteria, Campilobacterota and Bacteroidota were the major microbial phylum detected in the jejunum content. Firmicutes were the dominant phylum for 4- and 7-days jejunum control groups accounting for (>60% of the sequences). In the infected group Campilobacterota was the dominant phylum in the jejunum (> 24% of sequences) at 4-and 7-days post-infection groups, while Proteobacteria was predominant at 4- and 7-days post-infection of the cecum (> 40% of the sequences). The microbial genus Lactobacillus and Helicobacter were found in the jejunum, while Alistipes, Barnesiella and Faecalibacterium were detected in the cecum. In the jejunum, Helicobacter was dominant at 4 -and-7 days post-infection (≥24%), and Lactobacillus was dominant at 4 -and 7- days in the control group (> 50%). In 4- and 7-days post-infection, Alistipes genus was the more prevalent (> 38%) in the cecum. Thus, clear differences were observed in the bacterial microbiota distribution and abundance between the jejunum and cecum, as well as between infected and control groups for both tissues. The results indicate that chicken intestinal microbial imbalance (dysbiosis) is associated with Eimeria parasite infection and will likely affect the host-microbial non-pathogenic and pathogenic molecular interactions.

Metagenomic shotgun sequencing and metabolomic profiling identify specific human gut microbiota associated with diabetic retinopathy in patients with type 2 diabetes

Background

Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM) and is one of the leading causes of blindness among DM patients. However, the molecular mechanism involving DR remains unclear.

Methods

A case–control study with age-, sex-, and duration-matched diabetic patients and controls was conducted, which included 15 type 2 DM (T2DM) patients with DR and 15 T2DM patients without DR. Shotgun sequencing and non-targeted metabolomic profiling analyses of fecal samples were performed, and comprehensive bioinformatics analyses were conducted.

Results

Using metagenomic analyses, we identified 293,460 unique genes in the non-DR group, while that in the DR group was 283,235, and the number of overlapping genes was 1,237,914. Regarding phylum levels, Actinobacteria decreased but Bacteroidetes increased in the DR group when compared with those in the control group. Regarding genus levels, Bifidobacterium and Lactobacillus decreased. Cellular processes, environmental information processes, and metabolism-related pathways were found at higher levels in the gut microbiome of DR patients. Using metabolomic analyses, we found 116 differentially expressed metabolites with a positive ion model and 168 differentially expressed metabolites with a negative ion model between the two groups. Kyoto Encyclopedia of Genes and Genomes annotation revealed six pathways with different levels between DR and diabetic controls, namely, cellular processes, environmental information processing, genetic information processing, human diseases, organismal systems and metabolism. Moreover, lysine biosynthesis and lysine degradation were enriched using a positive model, but histidine metabolism and β-alanine metabolism were enriched using a negative model.

Conclusions

Together, the metagenomic profiles of DR patients indicated different gut microbiota compositions and characteristic fecal metabolic phenotypes in DR patients. Our findings of microbial pathways therefore provided potential etiological and therapeutic targets for DR patients.

Investigating the effects of environment, corrosion degree, and distribution of corrosive microbial communities on service-life of refined oil pipelines

Although the potential corrosive microbial communities of the refined oil pipelines can cause pipeline failure which directly threatens on soil and water environment, few studies have been published in this field. Therefore, the long-distance on-site internal corrosion detection and high-throughput sequencing techniques were employed in this study to investigate the distribution shifts of the corrosive microbial communities on the inner wall of a refined oil pipeline and its impact on the internal corrosion. The microorganisms colonizing on the inner wall of the pipeline showed significant distribution differences between the axial direction of the relative elevation and radial direction of the cross-section. On the inner wall, the high diversity and the abundance of the corrosive microbial communities induced serious microbiologically influenced corrosion (MIC), while the chemical corrosion and the synergy of the corrosive microbial communities accelerated the internal corrosion of the refined oil pipeline. A corrosion zone model has been proposed, which divides the pipeline cross-section into the sediment, the water-oil interface, the gas-oil interface, and the oil fully immersed zones. Therefore, the relationships between the environment, corrosion degree, and distribution characteristics of the corrosive microbial communities in the pipeline were analyzed. This research exhibited the importance of the distribution characteristics of the corrosive microorganisms on the inner wall of the refined oil pipelines. Its internal corrosion behavior was accurately explored, while providing a basis for controlling the corrosive microbial communities.

Comparative Analysis of the Gut Microbiota of Mongolian Gazelle (Procapra gutturosa) Under Fragmented Habitats

The existence of man-made facilities such as pasture fences makes the grassland ecosystem fragmented and endangers the survival of local wild animals. The Mongolian gazelle is highly sensitive to hunting and habitat destruction, and is one of the most threatened artiodactyls in Eurasia. It provides a critical model to studying gut microbiota under fragmented habitats. Therefore, we applied metagenomics sequencing to analyze the gut microbiota communities and functions of Mongolian gazelle under fragmented habitats. The results demonstrated that there were no significant differences in gut microbial communities between the different groups at both the phylum and genus level. The functional analyses showed that the Mongolian gazelle in fragmented habitat had a stronger ability to degrade naphthalene, but their ability to absorb carbohydrates was weaker. This study provided fundamental information about the gut microbiota of Mongolian gazelle, and we recommend reducing habitat fragmentation to better protect the Mongolian gazelle.

Study on the effect of koumiss on the intestinal microbiota of mice infected with Toxoplasma gondii

Toxoplasma gondii is a worldwide food-borne parasite that can infect almost all warm-blooded animals, including humans. To date, there are no effective drugs to prevent or eradicate T. gondii infection. Recent studies have shown that probiotics could influence the relationship between the microbiota and parasites in the host. Koumiss has been used to treat many diseases based on its probiotic diversity. Therefore, we explored the effect of koumiss on T. gondii infection via its effect on the host intestinal microbiota. BALB/c mice were infected with T. gondii and treated with PBS, koumiss and mares' milk. Brain cysts were counted, and long-term changes in the microbiota and the effect of koumiss on gut microbiota were investigated with high-throughput sequencing technology. The results suggested that koumiss treatment significantly decreased the cyst counts in the brain (P < 0.05). Moreover, T. gondii infection changed the microbiota composition, and koumiss treatment increased the relative abundance of Lachnospiraceae and Akkermansia muciniphila, which were associated with preventing T. gondii infection. Moreover, koumiss could inhibit or ameliorate T. gondii infection by increasing the abundance of certain bacteria that control unique metabolic pathways. The study not only established a close interaction among the host, intracellular pathogens and intestinal microbiota but also provided a novel focus for drug development to prevent and eradicate T. gondii infection.

Identification of tick-borne pathogens using metagenomic analyses in H. longicornis feeding on humans in downtown Beijing

On August 14th, 2018, a Beijing resident living in Xicheng District found a female H. longicornis tick attached to the skin at the front of his upper shin. On examination, the patient was afebrile and appeared well. The species of the tick was identified through morphological characteristics and phylogenetic analysis based on cytochrome C oxidase subunit I. This H. longicornis tick was screened for tick-borne pathogens such as viruses, bacteria and parasites. RNA pathogens were screened by PCR and sequencing, while DNA pathogens were screened by metagenomic analyses. It was found that the tick was positive for the DNA sequences of zoonotic and animal pathogens such as A. phagocytophilum, Ehrlichia minasensis and C. burnetii. Considering the good health condition of the patient, we hypothesized that the pathogens originated from the tick specimen itself rather than host blood meal. For the first time, our study reveals the possible risk of transmission of tick-borne pathogens to human beings through tick bit in downtown Beijing. Further research is needed to screen for tick-borne pathogens among unfed ticks collected from central Beijing.

Altered fecal microbiota composition in individuals who abuse methamphetamine

As a severe public health problem, methamphetamine (METH) abuse places a heavy burden on families and society. A growing amount of evidence has indicated communication between gut microbiota and the CNS in drug addiction, with associations to neural, endocrine and immune pathways. Thus, we searched for alterations in the gut microbiota and their potential effects in METH users through 16S rRNA gene sequencing. A decreased Shannon index indicated lower bacterial diversity in the METH users than in the age-matched control group. The gut microbial community composition in the METH users was also altered, including reductions in Deltaproteobacteria and Bacteroidaceae abundances and increases in Sphingomonadales, Xanthomonadales, Romboutsia and Lachnospiraceae abundances. Moreover, the Fusobacteria abundance was correlated with the duration of METH use. Enterobacteriaceae, Ruminococcaceae, Bacteroides, and Faecalibacterium had statistically significant correlations with items related to the positive and negative symptoms of schizophrenia and to general psychopathology in the METH users, and all have previously been reported to be altered in individuals with psychotic syndromes, especially depression. Abstraction, one of the items of the cognitive assessment, was positively related to Blautia. These findings revealed alterations in the gut microbiota of METH users, and these alterations may play a role in psychotic syndrome and cognitive impairment. Although the mechanisms behind the links between these disorders and METH abuse are unknown, the relationships may indicate similarities in the pathogenesis of psychosis induced by METH abuse and other causes, providing a new paradigm for addiction and METH use disorder treatment.

Inhibitory Effect of Garcinol on Obesity-Exacerbated, Colitis-Mediated Colon Carcinogenesis

SCOPE

Epidemiological studies show a consistent and compelling association between the risk of colorectal cancer development and obesity, but its mechanisms remain poorly understood. Evidence is mounting that colorectal cancer can be prevented by nutritional supplements, such as phytochemicals. Garcinol, a polyisoprenylated benzophenone derivative, is widely present in Garcinia plants. This study investigates the potential role of garcinol supplementation in ameliorating obesity-induced colon cancer development.

METHODS AND RESULTS

An animal model to investigate the effect of high-fat-diet (HFD)-induced obesity on promoting colitis-associated colon cancer (AOM (azoxymethane)/DSS (dextran sodium sulfate)-induced) is designed. The results show that HFD can promote colitis-associated colon cancer as compared to an AOM/DSS group without the intervention of obesity, and supplementing with 0.05% garcinol in the diet can significantly ameliorate obesity-promoted colon carcinogenesis. The results also reveals that the microbiota composition of each group is significantly different and clustered. The most representative genera are Alistipes, Romboutsia, and Ruminococcus. The RNA-sequencing results show that the administration of garcinol can regulate genes and improve obesity-promoting colitis-associated colon carcinogenesis.

CONCLUSION

The study results suggest that garcinol can prevent obesity-promoted colorectal cancer, and these findings provide important niches for the future development of garcinol as functional foods or adjuvant therapeutic agents.

Irrigation has a higher impact on soil bacterial abundance, diversity and composition than nitrogen fertilization

The aim of this study was to assess the effects of irrigation frequency and nitrogen fertilization rate on the abundance, diversity, and composition of soil bacteria in winter wheat. Irrigation, but not nitrogen fertilization, significantly affected the bacterial alpha diversity index. Among the 50 phyla obtained in these treatments, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Firmicutes were the predominant phyla. The LEfSe analysis of different treatments indicated that irrigation had a stronger effect on soil bacteria community composition than nitrogen fertilization. Moreover, the soil pH, moisture, available phosphorus (AP), and available potassium (AK) significantly correlated with the relative abundance of dominant bacteria at the phylum, genus, and operational taxonomic unit (OTU) levels. Overall, after three years of irrigation and fertilization treatments, the effect of irrigation on soil bacteria abundance, diversity, and composition of winter wheat was stronger than that of nitrogen fertilization, highlighting the importance of water availability for bacteria communities in semi-arid ecosystems. Inorganic and organic fertilizers should be applied in rotation.

High-Throughput Sequencing Reveals Bacterial Diversity in Raw Milk Production Environment and Production Chain in Tangshan City of China

Raw milk is a nature media of microbiota that access milk from various sources, which constitutes a challenge in dairy production. This study characterizes the relationship between the raw milk quality and the bacteria diversity at different sampling sites in dairy farms, aiming to provide a strong scientific basis for good hygienic practices and optimized procedure in milk production. High-throughput sequencing of 16S rRNA V3-V4 region was used to analyze the components, abundance and diversity of 48 bacterial population sampled from 8 different sites in dairy farm: pre-sterilized cow’s teats (C1), post-sterilized cow’s teats (C2), milking cluster (E), milk in storage tank (M1), transport vehicle (M2), storage equipment (E2), cow’s dung samples (F) and drinking water (W). Firmicutes account for predominantly 32.36% (C1), 44.62% (C2), 44.71% (E), 41.10% (M1), 45.08% (M2), 53.38% (F) of all annotated phyla. Proteobacteria accounts for 81.79% in W group and Actinobacteria 56.43% in E2 group. At the genus level, Acinetobacter was the most abundant genus that causes bovine mastitis, Acinetobacter and Arthrobacter were dominant in C1, C2, and E groups, Kocuria in E2 group and Arcobacter in W group. E, C1, and C2 group have very similar bacterial composition, and M1 and M2 demonstrated similar composition, indicating that the milking cluster was polluted by the environment or contact with cow udders. Bacterial population composition in different sampling sites identified by NGS reveals a correlation between the bacteria communities of raw milk production chain and the quality of raw milk.

Pathological Impact on the Phyllosphere Microbiota of Artemisia argyi by Haze

The pathological impact of haze upon the phyllosphere microbiota awaits investigation. A moderate degree of haze environment and a clean control were selected in Chengdu, China. Artemisia argyi, a ubiquitously distributed and extensively applied Chinese herb, was also chosen for experiment. Total genome DNA was extracted from leaf samples, and for metagenome sequencing, an Illumina HiSeq 2500 platform was applied. The results showed that the gene numbers of phyllosphere microbiota derived from haze leaves were lower than those of the clean control. The phyllosphere microbiota derived from both haze and clean groups shared the same top ten phyla; the abundances of Proteobacteria, Actinomycetes and Anorthococcuso of the haze group were substantially increased, while Ascomycetes and Basidiomycetes decreased. At the genus level, the abundances of Nocardia, Paracoccus, Marmoricola and Knoelia from haze leaves were markedly increased, while the yeasts were statistically decreased. KEGG retrieval demonstrated that the functional genes were most annotated to metabolism. An interesting find of this work is that the phyllosphere microbiota responsible for the synthesis of primary and secondary metabolites in A. argyi were significantly increased under a haze environment. Relatively enriched genes annotated by eggNOG belong to replication, recombination and repair, and genes classified into the glycoside hydrolase and glycosyltransferase enzymes were significantly increased. In summary, we found that both structure and function of phyllosphere microbiota are globally impacted by haze, while primary and secondary metabolites responsible for haze tolerance were considerably increased. These results suggest an adaptive strategy of plants for tolerating and confronting haze damage.

Identification of the Potential Role of the Rumen Microbiome in Milk Protein and Fat Synthesis in Dairy Cows Using Metagenomic Sequencing

Simple Summary

The rumen is the main digestive and absorption organ of dairy cows. It contains abundant microorganisms and can effectively use human-indigestible plant mass. Therefore, we used metagenomics to explore the role of rumen microbes in the regulation of milk protein and fat in dairy cows. This study showed that Prevotella species and Neocallimastix californiae in the rumen of cows are related to the synthesis of milk components due to their important functions in carbohydrate, amino acid, pyruvate, insulin, and lipid metabolism and transportation metabolic pathways.

Abstract

The rumen contains abundant microorganisms that aid in the digestion of lignocellulosic feed and are associated with host phenotype traits. Cows with extremely high milk protein and fat percentages (HPF; n = 3) and low milk protein and fat percentages (LPF; n = 3) were selected from 4000 lactating Holstein cows under the same nutritional and management conditions. We found that the total concentration of volatile fatty acids, acetate, butyrate, and propionate in the rumen fluid was significantly higher in the HPF group than in the LPF group. Moreover, we identified 38 most abundant species displaying differential richness between the two groups, in which Prevotella accounted for 68.8% of the species, with the highest abundance in the HPF group. Functional annotation based on the Kyoto Encyclopedia of Gene and Genome (KEGG), evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG), and Carbohydrate-Active enzymes (CAZy) databases showed that the significantly more abundant species in the HPF group are enriched in carbohydrate, amino acid, pyruvate, insulin, and lipid metabolism and transportation. Furthermore, Spearman’s rank correlation analysis revealed that specific microbial taxa (mainly the Prevotella species and Neocallimastix californiae) are positively correlated with total volatile fatty acids (VFA). Collectively, we found that the HPF group was enriched with several Prevotella species related to the total VFA, acetate, and amino acid synthesis. Thereby, these fulfilled the host’s needs for energy, fat, and rumen microbial protein, which can be used for increased biosynthesis of milk fat and milk protein. Our findings provide novel information for elucidation of the regulatory mechanism of the rumen in the formation of milk composition.

Using Bioinformatics to Quantify the Variability and Diversity of the Microbial Community Structure in Pond Ecosystems of a Subtropical Catchment

Background:

In rural China, many natural water bodies and farmlands have been converted into fish farming ponds as an economic developmental strategy. There is still a limited understanding of how the diversity and structure of microbial communities change in nature and become managed fish pond ecosystems.

Objective:

We aimed to identify the changes of the diversity and structure of microbial community and driving mechanism in pond ecosystems.

Methods:

The datasets of 16S rRNA amplicon sequencing and the concentrations of N and P fractions were achieved in water samples of pond ecosystems. Bioinformatics analysis was used to analyze the diversity and structure of the microbial communities.

Results:

Our results indicated that the diversity and structure of the microbial communities in the natural ponds were significantly different from ones in managed fish ponds. The nutrients of N and P and water environmental factors were responsible for 46.3% and 19.5% of the changes in the structure and diversity of the microbial community, respectively.

Conclusion:

The N and P fractions and water environmental factors influenced the microbial community structure and diversity in pond ecosystems. Fish farming indirectly affected the microbial community by altering the contents of N and P fractions in water bodies of ponds, when a natural pond was converted into a managed fish pond.

Vitamin A Deficiency in the Early-Life Periods Alters a Diversity of the Colonic Mucosal Microbiota in Rats

Vitamin A deficiency (VAD) remains a public health issue worldwide, affecting pregnant women and children. The early-life microbiota is a potentially effective intervention target for modulating immune and metabolic development of the host. This paper investigates the effects of VAD during different life periods on the structure of the colonic mucosa microbiota in adolescent rats. The results showed that the concentrations of serum retinol were > ~1.05 μmol/L in maternal VA normal (VAN)rats and < 0.7 μmol/L in maternal VAD rats, while the serum retinol levels were higher than 0.7 μmol/L in the pups of the VAN group and below 0.5 μmol/L in the pups of the VAD group. Compared to the offspring persistent with VAN from embryonic stage (group A), all the remaining groups exhibited an increased ratio of Firmicutes/Bacteroidetes abundance. A metagenome analysis (LEfSe) and a differentially abundant features approach using Metastats for genus abundances revealed that Diaphorobacter and Psychrobacter were increased in the offspring persistent with VAD from embryonic stage (group B);Bifidobacterium was decreased and Staphylococcus was increased in the offspring with VAD after weaning (group C); Propionibacterium and Enterobacter were increased significantly in the offspring with VAD during gestation(group E); and Ochrobactrum was increased in group B and the offspring with VAD during gestation and lactation(group D). Faecalibacterium abundance was significantly and positively related to serum retinol levels, while that of Staphylococcus was significantly and negatively correlated with serum retinol levels. VAD in different life periods can alter the gut microbiome in rats, but VAD in the early-life periods (especially gestation and/or lactation) leads to a diversity of the colonic mucosal microbiota in adolescent rats as well as an imbalance of the ratio between Firmicutes and Bacteroidetes. The early-life period may become a time window of VA intervention to improve intestinal microbiota caused by VA deficiency, but the specific mechanism requires more in-depth research.

Gut Microbiota in Dholes During Estrus

The co-evolution of gut microbes and the host plays a vital role in the survival and reproduction of the host. The dhole (Cuon alpinus) has been listed as endangered species by the International Union for Conservation of Nature; therefore, conservation and effective breeding of dholes are essential. Effective estrus can promote reproduction. However, little is known about the relative contribution of estrus in shaping the structure and the functions of fecal microbiota. Here, we investigated the potential association between estrus and the fecal microbiota in dholes using shotgun metagenomic sequencing. We found that the estrus stages in dholes vary significantly in terms of gut bacterial composition and microbiome metabolism and function. Compared with that of non-estrus, adult dholes, the microbiome of estrus adult dholes had a significantly higher abundance of Bacillus faecalis and Veillonella, which play a key role in the synthesis of sex hormones and nucleic acids, energy production, and reproductive cell division. The insulin and energy metabolism-related pathways are significantly enhanced in the gut microbes and the related gluconeogenic enzymes are significantly enriched during estrus. These findings suggest that the structure and metagenome of the fecal microbiome during estrus have a significant effect in promoting estrus in dholes, thus providing a new perspective for dhole conservation.

Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing

In this study, a total of 14 vaginal samples (GPV1‐14) from giant pandas were analyzed. These vaginal samples were divided into two groups as per the region and age of giant pandas. All the vaginal samples were analyzed using metagenomic sequencing. As per the outcomes of metagenomic analysis, Proteobacteria (39.04%), Firmicutes (5.27%), Actinobacteria (2.94%), and Basidiomycota (2.77%) were found to be the dominant phyla in the microbiome of the vaginal samples. At the genus level, Pseudomonas (21.90%) was found to be the most dominant genus, followed by Streptococcus (3.47%), Psychrobacter (1.89%), and Proteus (1.38%). Metastats analysis of the microbial species in the vaginal samples of giant pandas from Wolong Nature Reserve, Dujiangyan and Ningbo Youngor Zoo, and Ya'an Bifengxia Nature Reserve was found to be significantly different (p < 0.05). Age groups, that is, AGE1 (5‐10 years old) and AGE2 (11‐16 years old), also demonstrated significantly different inter‐group microbial species (p < 0.05). For the first time, Chlamydia and Neisseria gonorrhoeae were detected in giant pandas’ reproductive tract. GPV3 vaginal sample (2.63%) showed highest Chlamydia content followed by GPV14 (0.91%), and GPV7 (0.62%). GPV5 vaginal sample (7.17%) showed the highest Neisseria gonorrhoeae content, followed by GPV14 (7.02%), and GPV8 (6.50%). Furthermore, we employed eggNOG, CAZy, KEGG, and NCBI databases to investigate the functional significance of giant panda's vaginal microbial community. The outcomes indicated that giant panda's vaginal microbes were involved in biological processes. The data from this study will help in improving the reproductive health of giant pandas.

Archaeal community diversity in different types of saline-alkali soil in arid regions of Northwest China

High-throughput sequencing was used to investigate the archaeal community structure and diversity, and associated influencing factors in the 5 subtypes and 13 genera of saline-alkali soil in Gansu Province, China. The results indicated the analysis of chemical parameters demonstrated statistically significant differences in these soils. Operational taxonomic units (OTUs), Chao 1, ACE, Simpson, and Shannon indexes of the archaeal community varied significantly in the 5 subtypes and 12 genera of soil except for chloride-type orthic solonchaks. The abundance was highest for sulfate-chloride-type meadow solonchaks and lowest for chloride-sulfate-type dry solonchaks. The diversity was highest for chloride-sulfate-type orthic solonchaks and lowest for sulfate-type orthic solonchaks. The archaeal community was dominated by the Euryarchaeota and Crenarchaeota. Except chloride-type orthic solonchaks; Halomicrobium in chloride-type meadow solonchaks (12.7%); Halobacterium in sulfate-chloride-type and chloride-sulfate-type dry solonchaks (11.1% and 9.2%, respectively); Candidatus Nitrososphaera in sulfate-chloride-type, chloride-sulfate-type, and sulphate-type meadow solonchaks; sulfate-type orthic solonchaks; and chloride bog solonchaks (9.0%, 21.6%, 27.0%, 45.3%, and 30.0%, respectively); Halorhabdus in sulfate-chloride-type orthic solonchaks, magnesium alkalized solonchaks, chloride-type dry solonchaks (15.7%, 11.5%, and 5.9%, respectively); and Haloarcula in chloride-sulfate-type orthic solonchaks (8.1%) were the most dominant archaea. Redundancy analysis showed that archaeal diversity was influenced by soil organic matter, total salt, sulfate anion, and zinc contents and pH. These results will lead to more comprehensive understanding of how 5 subtypes and 13 soil genera of saline-alkali soil affects microbial distribution.

Effects of Jian Pi Qu Shi Formula on intestinal bacterial flora in patients with idiopathic membranous nephropathy: A prospective randomized controlled trial

Background

The incidence of idiopathic membranous nephropathy (IMN) has recently increased remarkably. Immune dysfunction caused by disordered intestinal flora might be an important factor affecting IMN. The Jian Pi Qu Shi Formula (JPQSF) shows promise in treating IMN. Here, we sequenced 16S rRNA genes to compare intestinal flora between patients with IMN and healthy persons. We also conducted a randomized controlled clinical trial to further compare the intestinal flora of patients with IMN treated with traditional Chinese medicine (TCM) and western medicine (WM).

Methods

Among 40 patients with IMN treated at Department of Nephrology in Xiyuan Hospital, Chinese Academy of Traditional Chinese Medicine between July 2016 and December 2018, we compared 30 of them with 10 healthy persons (controls). The IMN group was randomly assigned to receive JPQSF (TCM) or immunosuppressant WM therapy in (n = 15 per group) for 6 months. Intestinal microbiota diversity was analyzed using alpha diversity and beta diversity. Intestinal flora that significantly differed between the groups was analyzed using MetaStat. The effects and safety of the therapies were determined based on the values for plasma albumin, 24-h urine protein excretion, serum creatinine, urea nitrogen, estimate glomerular filtration rate (eGFR), complete blood count, and liver enzymes. All data were statistically analyzed using Statistical Package for the Social Sciences (SPSS) 20.0 statistical software.

Results

Baseline characteristics did not significantly differ between the IMN and healthy groups, or the TCM and WM groups. After six months of treatment, 24-h urinary protein significantly declined in the TCM and WM groups (before and after treatment: 3.24 ± 1.74 vs. 1.73 ± 1.85 g, P < 0.05 and 3.94 ± 1.05 vs. 1.91 ± 1.18 g, P < 0.05, respectively). Plasma albumin was significantly increased in the TCM group (before vs. after treatment: 32.44 ± 9.04 vs. 39.99 ± 7.03 g/L, P < 0.05), but did not significantly change in the WM group (31.55 ± 4.23 vs. 34.83 ± 9.14 g/L, P > 0.05). Values for urea nitrogen, serum creatinine, and eGFR did not significantly change in either group. The alpha diversity index for intestinal flora differed between the IMN and healthy groups, and the TCM and WM groups. Comparisons of multiple samples (beta diversity) revealed differences in intestinal flora between the IMN and healthy groups, and the TCM and WM groups. The Metastat analysis findings showed that the main genera that differed between the IMN group before treatment and the healthy group were Christensenellaceae_R-7_group, Bifidobacterium (77), Dorea, Escherichia-Shigella, Parabacteroides, Bifidobacterium, and Coprococcus_3. After TCM therapy, the main differential genera were Butyricimonas, Bacteroides, Alistipes, and Lachnospira, and after WM therapy, these were Ruminococcus_2, Lachnospiraceae_ND3007_group, Lachnospira, Bifidobacterium, Alistipes, and [Eubacterium]_ventriosum_group.

Conclusion

Patients with IMN might have disordered intestinal flora, and JPQSF can regulate intestinal flora in patients with IMN.

Investigation on the influence of isolated environment on human psychological and physiological health

Crewmembers are working and living in isolated environment lacking natural light and perception. Although their health problems have been documented, the mechanism has not been thoroughly investigated. The aim of the present study is to investigate the psychological and physiological influences of isolated environment on crewmember's health. On account of complexity of the isolated environment, it is necessary to have a manually controllable system to simulate research platform-Bioregenerative Life Support System (BLSS). Symptom checklist 90 (SCL-90) was used to complete emotional status test. Urine samples were collected for metabonomics and hormone secretion analysis. Fecal samples were collected for intestinal microorganisms analysis. Crewmembers (n = 4) followed strict daily schedule during the experimental period. Five emotional factors were significantly (P < 0.05) increased, differential metabolites were enriched in tryptophan metabolism pathway, the relative abundance of Prevotella decreased significantly (P < 0.0001) when crewmembers in isolated environment without natural light. Hormone (melatonin, cortisol) secretion rhythm also changed. Significant positive correlation (r = 0.805, P < 0.05) between cortisol secretion and anxiety was observed. In conclusion, natural light simulation in an isolated environment may have a positive effect on the physiological and psychological health of the crewmember.

Potential Correlation between Dietary Fiber-Suppressed Microbial Conversion of Choline to Trimethylamine and Formation of Methylglyoxal

Dietary interventions alter the formation of the disease-associated metabolite, trimethylamine (TMA), via intestinal microbial TMA lyase activity. Nevertheless, the mechanisms regulating microbial enzyme production are still unclear. Sequencing of the gut bacteria 16S rDNA demonstrated that dietary intervention changed the composition of the gut microbiota and the functional metagenome involved in the choline utilization pathway. Characterization of the functional profile of the metagenomes and metabonomics analysis revealed that a series of Kyoto Encyclopedia of Genes and Genomes orthologous groups and enzyme groups related to accumulation of methylglyoxal (MG) and glycine were enriched in red meat diet-fed animals, whereas fiber-rich diet suppressed glycine formation via the MG-dependent pathway. Our observations suggest associations between choline-TMA lyase expression and MG formation, which are indicative of a novel role of the gut microbiota in choline metabolism and highlight it as a potential target for inhibiting TMA production.

Rearing pattern alters porcine myofiber type, fat deposition, associated microbial communities and functional capacity

BACKGROUND

The Chinese believe that the meat of pigs reared in the past with free range tastes better than that of the pigs reared indoor on a large scale today. Gastrointestinal microflora is closely associated with the main factor of meat flavour, including fibre characteristics and lipid metabolism. Our method in this study involved different raising patterns within the semi free-grazing farm (FF) or indoor feeding farm (DF), the measurement of fat deposition and myofiber type by paraffin section and reverse transcription polymerase chain reaction and the identification of microbiome and functional capacities associated with meat quality through metagenomic sequencing.

RESULTS

Results showed that the fat area in muscle and adipose tissue and the myofiber density significantly increased in the pigs of the FF group. The relative abundance of bacteria associated with lipid metabolism, such as g_Oscillibacter, in the feces of the FF group was higher than that in DF group, and the relative abundance of some bacteria with probiotic function, including g_Lactobacillus and g_Clostridium, was lower than that in DF group. The abundance of g_Clostridium was significantly positively correlated with the intramuscular fat area, whereas health-related bacteria, such as g_Butyricicoccus, g_Eubacterium, g_Phascolarctobacterium and g_Oribacterium, was significantly negatively correlated with abdominal fat area, myofiber density and adipose triglyceride lipase (ATGL) mRNA expression. KEGG analysis showed that pigs raised in semi free-grazing farm can activate the pathway of inosine monophosphate (IMP) biosynthesis, glycolysis/gluconeogenesis and alanine, aspartate and glutamate metabolism.

CONCLUSIONS

Free range feeding improves meat quality by changing the fibre type, myofiber density and metabolic pathways related to flavour amino acids, IMP or glycolysis/gluconeogenesis in muscle. However, prolonged feeding cycle increases fat deposition and associated microbial communities.

Changes in cecal microbiota community of suckling piglets infected with porcine epidemic diarrhea virus

Diarrhea, caused by porcine epidemic diarrhea virus (PEDV), is a catastrophic gastrointestinal disease among suckling piglets, with high infectivity, morbidity, and mortality, causing huge economic losses to the pig industry. In the present study, we investigated the different microbiota from the cecal mucosa and cecal contents between healthy and PEDV-infected piglets. High-throughput 16S rRNA gene sequencing was performed to explore differences. The results revealed that microbial dysbiosis by PEDV infection occurred in the cecal mucosa and contents of suckling piglets at each microbial taxonomic level. The abundance of pathogenic bacteria associated with diseases, including diarrhea, was increased. The abundance of Fusobacterium was 26.71% and 33.91% in cecal mucosa and contents of PEDV-infected group, respectively, whereas that in the healthy groups was 17.85% and 9.88%. The proportion of Proteobacteria in the infected groups was relatively high (24.67% and 22.79%, respectively), whereas that in the healthy group was 13.13% and 11.34% in the cecal mucosa and contents, respectively. Additionally, the proportion of Bacteroidetes in the healthy group (29.89%, 37.32%) was approximately twice that of the PEDV-infected group (15.50%, 15.39%). “Nitrate reduction”, “Human pathogens diarrhea”, “Human pathogens gastroenteritis”, “Nitrite respiration”, and “Nitrite ammonification” were the enriched functional annotation terms in the PEDV-infected groups. Porcine epidemic diarrhea virus infection increased the proportion of harmful bacteria and decreased the proportion of beneficial bacteria in the cecal mucosa and contents of suckling piglets. Our findings suggest that determining the intestinal microbiota might provide a promising method to prevent PEDV and open a new avenue for future research.

The microbiota profile and transcriptome analysis of immune response during metamorphosis stages in orange spotted grouper (Epinephelus coioides)

Metamorphosis is a transformation process in larval development associated with changes in morphological and physiological features, including the immune system. The gastrointestinal tract harbors a plethora of bacteria, which might affect the digestion and absorption of nutrients, immunity, and gut-brain crosstalk in the host. In this study, we have performed metagenomic and transcriptomic analyses on the intestines of grouper at the pre-, mid- and post-metamorphosis stages. The sequencing data of 16S rRNA gene showed drastic changes in the microbial communities at different developmental stages. The transcriptomic data revealed that the leukocyte transendothelial migration and the phagosome pathways might play important roles in mediating immunity in grouper at the three developmental stages. This information will increase our understanding of the metamorphosis process in grouper larvae, and shed light on the development of antimicrobial strategy during larval development.

Impact of DNA extraction methods on the observed microbial communities from the intestinal flora of the penaeid shrimp Litopenaeus vannamei

Two DNA extraction methods, the Zirmil-beating cell disruption method (ZBC) and the QIAamp fast DNA stool mini kit (QIA), were used to extract DNA from the intestinal flora of the penaeid shrimp Litopenaeus vannamei, and their microbial communities were analyzed using 16S rDNA high-throughput sequencing. Results were obtained in terms of the number of reads, alpha diversity indexes, beta diversity indexes and taxonomic composition. The alpha diversity indexes of the community, according to the ZBC method, were higher than those according to the QIA method. Furthermore, results from the three samples using the ZBC method were less consistent than those where the QIA method was used. Further, using the latter method led to substantive clustering. It is suggested that the QIA method is more stable and repeatable than the ZBC method. Although the two extraction methods shared the major abundant microflora based on 16S rDNA high-throughput sequencing, bias associated with diversity analysis indexes and certain species was observed.

Consumption of post-fermented Jing-Wei Fuzhuan brick tea alleviates liver dysfunction and intestinal microbiota dysbiosis in high fructose diet-fed mice

Emerging evidence supports the health-promoting ability of a special microbial-fermented Fuzhuan brick tea. Epigallocatechin gallate was identified as a dominant flavonoid of Fuzhuan tea aqueous extract (FTE). Mice were treated with 30% high fructose (HF) water feeding alone or in combination with administration of FTE at 400 mg per kg bw for 13 weeks. FTE caused strong inhibition against the elevation of liver weight, serum enzymatic (aspartate aminotransferase, aspartate aminotransferase and alkaline phosphatase) activities and hepatic inflammatory cytokines (interleukin-1, interleukin-6, tumor necrosis factor-α and tumor necrosis factor-β) formation, as well as dyslipidemia (total cholesterol, total triglyceride, low-density lipoprotein-cholesterol and high-density lipoprotein-cholesterol) in HF-fed mice (p < 0.05). Hepatic malonaldehyde formation was lowered, while superoxide dismutase and glutathione peroxidase activities were enhanced by FTE treatment, relative to HF-fed mice (p < 0.05), and histopathological evaluation confirmed the protection. As revealed by 16S rDNA gene sequencing, FTE notably increased abundance of Bacteroidetes and Lactobacillus, but reduced population of Firmicutes, Proteobacteria and Tenericutes in HF feeding mice. These findings suggest that FTE exerts a hepatoprotective effect by modifying hepatic oxidative stress, inflammatory response and gut microbiota dysfunction.

Fuzhuan brick tea can improve non-alcoholic fatty liver disease (NAFLD) and intestinal microbiota imbalance induced by a high fructose diet (HFD) intake in mice.

Regulating Gut Flora Dysbiosis in Obese Mice by Electroacupuncture

Recently, gut flora has been linked to the onset of obesity and has been shown to influence the host's metabolism. Acupuncture is a well-known agent used for the treatment of numerous diseases such as obesity. This study aimed to explore the impacts of electroacupuncture treatment on gut microbiota composition and function in obese mice. Pyrosequencing of 16S rRNA genes and Metagenomic analysis of the fecal microbiota were used for this purpose. The basic parameters of body weight, Lee's index, serum lipid and epididymal adipose weight were ameliorated significantly after introducing an electroacupuncture intervention. Acidobacteria, Cyanobacteria and Basidiomycota (Normal group) and Fusobacteria, Firmicutes and Spirochmycetes (Model group) were remarkably affluent at the phylum level. Bacteroides sp. CAG: 927 and Prevotella sp. CAG: 1031 (Normal group), Lachnospiraceae bacterium and Helicobacter rodentium (Model group) at the species level were distinctly enriched. The structures and functions of the intestinal flora were significantly different between healthy and obese mice, and animals in the acupuncture group gradually tended towards healthy controls. Moreover, electroacupuncture altered the bacterial diversity and metabolic genes to establish new balance, observed the obvious change from 7[Formula: see text]d and stabilized gradually through 21[Formula: see text]d. These findings suggested gut flora could be a novel target of electroacupuncture treatment against obesity.