Functional Metagenome Research Articles

Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China

To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3− increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N′-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.

Metagenomic Insight Reveals the Microbial Structure and Function of the Full-Scale Coking Wastewater Treatment System: Gene-Based Nitrogen Removal

Microbial communities play crucial roles in pollutant removal and system stability in biological systems for coking wastewater (CWW) treatment, but a comprehensive understanding of their structure and functions is still lacking. A five month survey of four sequential bioreactors, anoxic 1/oxic 1/anoxic 2/oxic 2 (A1/O1/A2/O2), was carried out in a full-scale CWW treatment system in China to elucidate operational performance and microbial ecology. The results showed that A1/O1/A2/O2 had excellent and stable performance for nitrogen removal. Both total nitrogen (TN; (17.38 ± 6.89) mg·L−1) and ammonium–nitrogen (NH4+-N; (2.10 ± 1.34) mg·L−1) in the final biological effluent satisfied the Chinese national standards for CWW. Integrated analysis of 16S ribosome RNA (rRNA) sequencing and metagenomic sequencing showed that the bacterial communities and metagenomic function profiles of A1 and O1 shared similar functional structures, while those of A2 significantly varied from those of other bioreactors (p < 0.05). The results indicated that microbial activity was strongly connected with activated sludge function. Nitrosospira, Nitrosomonas, and SM1A02 were responsible for nitrification during the primary anoxic–oxic (AO) stage and Azoarcus and Thauera acted as important denitrifiers in A2. Nitrogen cycling-related enzymes and genes work in the A1/O1/A2/O2 system. Moreover, the hao genes catalyzing hydroxylamine dehydrogenase (EC 1.7.2.6) and the napA and napB genes catalyzing nitrate reductase (EC 1.9.6.1) played important roles in the nitrification and denitrification processes in the primary and secondary AO stages, respectively. The mixed liquor suspended solids (MLSS)/total solids (TS), TN removal rate (RR), total organic carbon (TOC) (RR), and NH4+-N (RR) were the most important environmental factors for regulating the structure of core bacterial genera and nitrogen-cycling genes. Proteobacteria were the potential main participants in nitrogen metabolism in the A1/O1/A2/O2 system for CWW treatment. This study provides an original and comprehensive understanding of the microbial community and functions at the gene level, which is crucial for the efficient and stable operation of the full-scale biological process for CWW treatment.

Duodenal microbiome in chronic kidney disease.

The intestinal microbiome is involved in the pathogenesis of chronic kidney disease (CKD). Despite its importance, the microbiome of the small intestinal mucosa has been little studied due to sampling difficulties, and previous studies have mainly focused on fecal sources for microbiome studies. We aimed to characterize the small intestinal microbiome of CKD patients by studying the microbiome collected from duodenal and fecal samples of CKD patients and healthy controls. Overall, 28 stage 5 CKD patients and 21 healthy participants were enrolled. Mucosal samples were collected from the deep duodenum during esophagogastroduodenoscopy and fecal samples were also collected. The 16S ribosomal RNA gene sequencing using Qiime2 was used to investigate and compare the microbial structure and metagenomic function of the duodenal and fecal microbiomes. The duodenal flora of CKD patients had decreased alpha diversity compared with the control group. On the basis of taxonomic composition, Veillonella and Prevotella were significantly reduced in the duodenal flora of CKD patients. The tyrosine and tryptophan metabolic pathways were enhanced in the urea toxin-related metabolic pathways based on the Kyoto Encyclopedia of Genes and Genomes database. The small intestinal microbiome in CKD patients is significantly altered, indicating that increased intestinal permeability and production of uremic toxin may occur in the upper small intestine of CKD patients.

Sustainable Use of Organic Seaweed Fertilizer Improves the Metagenomic Function of Microbial Communities in the Soil of Rice Plants

The frequent use of chemical fertilizers in agricultural practices has developed into a serious environmental concern which urgently needs a solution to restrain their use in agricultural systems. Hence, there is an urgent need to investigate potential organic fertilizers from various natural resources to decrease the use of chemical fertilizers. Seaweed is among the natural resources with potential sustainability value. Our previous work has shown the effectiveness of seaweed fertilizer for increasing plant growth and soil beneficial microbiota. This study aims to evaluate the functional genes present in the soil of rice plants treated with seaweed fertilization. It involves amendments with reduced concentrations of chemical fertilizer in three groups: CF (only chemical fertilizer), CFSF1 (50% dose of CF + seaweed fertilizer 1 ton/ha), and CFSF2 (50% dose of CF + seaweed fertilizer 2 ton/ha). The rice plants supplemented with CFSF1 and CFSF2 were taller and faster to mature compared to CF. In addition, the primary macronutrients nitrogen (N), phosphorus (P), and potassium (K) were also significantly higher in soil supplemented with SF. Our findings showed increased ammonia-oxidizing archaea Crenarchaeota abundance in increasing SF treatments. The PICRUSt analyses indicated enriched functional genes and proteins in relation to amino acid, nucleotide, protein, and carbohydrate metabolism based on the KEGG, BioCyc, and PFAM databases. The current outcomes enhanced our understanding regarding the importance of microbial community for soil quality. Furthermore, seaweed supplementation has shown improvement in soil fertility, which significantly increases rice plant growth and productivity.

OA susceptibility in mice is partially mediated by the gut microbiome, is transferrable via microbiome transplantation and is associated with immunophenotype changes

ObjectivesThe Murphy Roths Large (MRL)/MpJ ‘superhealer’ mouse strain is protected from post-traumatic osteoarthritis (OA), although no studies have evaluated the microbiome in the context of this protection. This study characterised...

Sex-specific aging patterns of gut microbiota guild in urban Chinese adults

Abstract Background The loss of gut microbial stability has been observed during aging. Previous studies have noted changes in the diversity of gut microbiota and richness of specific bacteria along with age, but rarely focused on alternations in microbial guild. Methods Included in this study were 2944 middle-aged and elderly Chinese adults (1473 men and 1471 women) from the Shanghai Men's and Women's Health Studies, of whom 1419 healthy subjects (747 men and 672 women) self-reported no common non-communicable diseases (NCD) were selected for evaluating the healthy aging pattern. Microbiome was profiled by 16S rRNA sequencing. A guild-based method was adopted to cluster operational taxonomic units (OTU) into co-abundance groups (CAG) as functional units. PICRUSt2 were used to predict metagenome functions. The aging trend were assessed by linear regression. A random forest model incorporating significant CAGs with chronological age was developed to fit microbial age in the healthy and subsequently applied to those with NCDs. Results The age of all participants ranged from 51.4 to 89.3 years (mean of 70.2). A decline in Chao1 index and an increase in Pielou evenness with aging were observed among healthy women but not men. The microbial drift based on Bray-Curtis distance appeared driven by age and differed significantly by sex. Eleven CAGs were identified as potential aging markers in men, and twelve in women; wherein only CAG_6 (Bifidobacterium sp. dominated) and CAG_118 (Veillonella dispar dominated) were positively related with age in both genders. The 1,4-dihydroxy-2-naphthoate biosynthesis served as the core metabolic pathway that increased with age in both men and women. Subjects with metabolic diseases had an older microbial age than the healthy, particularly among men. Conclusions This study indicates the importance of gut microbiota in healthy aging among Chinese men and women. The aging related sex-specific patterns of gut microbiota can be modified by prevalent NCDs. Key messages • The aging patterns of gut microbiota guild were different in middle-aged and elderly Chinese men and women. • The microbial age was older in subjects with metabolic diseases than those without.

Joining the bacterial conversation: increasing the cultivation efficiency of soil bacteria with acyl-homoserine lactones and cAMP.

Bacteria need to be isolated in pure culture to gain access to the wide array of interesting functions they conceal. This is challenging because they do not live in isolation but instead in communities where they actively communicate and interact with each other. In this study, we aimed to increase the culturability of soil bacteria using three different signaling molecules: N-(3-oxohexanoyl)-L-homoserine lactone, N-octanoyl-L-homoserine lactone, and 3',5'-cyclic adenosine monophosphate (cAMP). The signals were added individually to soils suspended in PBS buffer to a final concentration of 5 µM. Soil suspensions were agitated for 24 hours, after which they were serially diluted and plated on tenfold-diluted Reasoner's 2A agar that either contained or did not contain the same signaling molecule used during the extraction step. DNA was isolated from both soil suspensions and grown cultures and, after a high-throughput amplicon sequencing, differences in bacterial abundances and diversity were determined across treatments. To further explain the action of the signaling molecules on the treated soil communities, their metagenomic functions were predicted using the software PICRUSt2. N-octanoyl-L-homoserine lactone was found to increase the diversity observed on solid media, while N-(3-oxohexanoyl)-L-homoserine lactone and cAMP were not. Potentially novel isolates aided by the signaling molecules were affiliated with the genera Pseudomonas and Nocardioides. IMPORTANCE Microorganisms are a repository of interesting metabolites and functions. Therefore, accessing them is an important exercise for advancing not only basic questions about their physiology but also to advance technological applications. In this sense, increasing the culturability of environmental microorganisms remains an important endeavor for modern microbiology. Because microorganisms do not live in isolation in their environments, molecules can be added to the cultivation strategies to "inform them" that they are present in growth-permissive environmental conditions. Signaling molecules such as acyl-homoserine lactones and 3',5'-cyclic adenosine monophosphate belong to the plethora of molecules used by bacteria to communicate with each other in a phenomenon called quorum sensing. Therefore, including quorum sensing molecules can be an incentive for microorganisms, specifically soil bacteria, to increase their numbers on solid media.

Blue Light-Emitting Diode Irradiation Without a Photosensitizer Alters Oral Microbiome Composition of Ligature-Induced Periodontitis in Mice.

Objective: This study investigated the suppressive effects of blue light-emitting diode (LED) irradiation on bone resorption and changes in the oral microbiome of mice with ligature-induced periodontitis. Background: Wavelength of blue light has antimicrobial effects; however, whether blue LED irradiation alone inhibits the progression of periodontitis remains unclear. Methods: Nine-week-old male mice ligated ligature around the right maxillary second molar was divided into ligation alone (Li) and ligation with blue LED irradiation (LiBL) groups. The LiBL group underwent blue LED (wavelength, 455 nm) irradiation four times in a week at 150 mW/cm2 without a photosensitizer on the gingival tissue around the ligated tooth at a distance of 5 mm for 5 min. The total energy density per day was 45 J/cm2. Bone resorption was evaluated using micro-computed tomography at 8 days. Differences in the oral microbiome composition of the collected ligatures between the Li and LiBL groups were analyzed using next-generation sequencing based on the 16S rRNA gene from the ligatures. Results: Blue LED irradiation did not suppress bone resorption caused by ligature-induced periodontitis. However, in the LiBL group, the α-diversity, number of observed features, and Chao1 were significantly decreased. The relative abundances in phylum Myxococcota and Bacteroidota were underrepresented, and the genera Staphylococcus, Lactococcus, and Lactobacillus were significantly overrepresented by blue LED exposure. Metagenomic function prediction indicated an increase in the downregulated pathways related to microbial energy metabolism after irradiation. The co-occurrence network was altered to a simpler structure in the LiBL group, and the number of core genera decreased. Conclusions: Blue LED irradiation altered the composition and network of the oral microbiome of ligature-induced periodontitis in mice.

Association of Pooled Fecal Microbiota on Height Growth in Children According to Enterotypes.

The association between fecal microbiota and height in children has yielded conflicting findings, warranting further investigation into potential differences in fecal bacterial composition between children with short stature and those of standard height based on enterotypes (ETs). According to the height z score for age and gender, the children were categorized into normal-stature (NS; n = 335) and short-stature (SS; n = 152) groups using a z score of -1.15 as a separator value. The human fecal bacterial FASTA/Q files (n = 487) were pooled and analyzed with the QIIME 2 platform with the National Center for Biotechnology Information alignment search tool. According to ETs, the prediction models by the machine learning algorithms were used for explaining SS, and their quality was validated. The proportion of SS was 16.4% in ET Enterobacteriaceae (ET-E) and 68.1% in Prevotellaceae (ET-P). The Chao1 and Shannon indexes were significantly lower in the SS than in the NS groups only in ET-P. The fecal bacteria related to SS from the prediction models were similar regardless of ETs. However, in network analysis, the negative correlations between fecal bacteria in the NS and SS groups were much higher in the ET-P than in the ET-E. In the metagenome function, fecal bacteria showed an inverse association of biotin and secondary bile acid synthesis and downregulation of insulin/insulin-like growth factor-1-driven phosphoinositide 3-kinase Akt signaling and AMP-kinase signaling in the SS group compared with the NS group in both ETs. The gut microbial compositions in children were associated with height. Strategies to modify and optimize the gut microbiota composition should be investigated for any potential in promoting height in children.

Microbial distribution and diversity along a vertical profile in the water column of a seasonal Oxygen minimum zone in the Southeast Arabian Sea

The Oxygen Minimum Zones (OMZ) support a milieu of microbial communities capable of degrading complex molecules. The current study reports the vertical distribution of microorganisms and diversity of bacteria in Arabian Sea OMZ, measured using fluorescence in situ hybridization (FISH) technique and 16S rRNA gene amplicon sequencing respectively. Bacterial and archaeal abundances were of the magnitude 104–105 and 103 cells ml−1 respectively. Proteobacteria was the most abundant phyla. The other phyla included were Bacteriodota, Actinobacteria, Verrucomicrobia, Marinimicrobia, Chloroflexi, Nitrospinota and SAR 324 clade. The results of alpha diversity analysis (Shannon and Chao1) of OTUs showed that the bacterial communities were different between physically close water masses at different depths in an OMZ. The predictive analysis of metagenome functions showed that the bacteria present in OMZ were able to metabolize different complex molecules such as polysaccharides, aromatic compounds, nucleosides, sulfur under hypoxic conditions in the OMZ. Overall, the results of the current study indicate the OMZ is a niche for a diverse group of bacteria which can process various complex metabolites. Further studies on the isolation and functional characterization of these microorganisms may be beneficial for exploring their biotechnological potentials.

Influence of Symbiotic Fermentation Broth on Regulating Metabolism with Gut Microbiota and Metabolite Profiles Is Estimated Using a Third-Generation Sequencing Platform.

Overnutrition with a high-fat or high-sugar diet is widely considered to be the risk factor for various metabolic, chronic, or malignant diseases that are accompanied by alterations in gut microbiota, metabolites, and downstream pathways. In this study, we investigated supplementation with soybean fermentation broth containing saponin (SFBS, also called SAPOZYME) in male C57BL/6 mice fed a high-fat-fructose diet or normal chaw. In addition to the lessening of weight gain, the influence of SFBS on reducing hyperlipidemia and hyperglycemia associated with a high-fat-fructose diet was estimated using the results of related biological tests. The results of gut microbial profiling indicated that the high-fat-fructose diet mediated increases in opportunistic pathogens. In contrast, SFBS supplementation reprogrammed the high-fat-fructose diet-related microbial community with a relatively high abundance of potential probiotics, including Akkermansia and Lactobacillus genera. The metagenomic functions of differential microbial composition in a mouse model and enrolled participants were assessed using the PICRUSt2 algorithm coupled with the MetaCyc and the KEGG Orthology databases. SFBS supplementation exerted a similar influence on an increase in the level of 4-aminobutanoate (also called GABA) through the L-glutamate degradation pathway in the mouse model and the enrolled healthy population. These results suggest the beneficial influence of SFBS supplementation on metabolic disorders associated with a high-fat-fructose diet, and SFBS may function as a nutritional supplement for people with diverse requirements.

The visceral adipose tissue bacterial microbiota provides a signature of obesity based on inferred metagenomic functions.

Metabolic inflammation mediated obesity requires bacterial molecules to trigger immune and adipose cells leading to inflammation and adipose depot development. In addition to the well-established gut microbiota dysbiosis, a leaky gut has been identified in patients with obesity and animal models, characterized by the presence of a tissue microbiota in the adipose fat pads. To determine its potential role, we sequenced the bacterial 16 S rRNA genes in the visceral adipose depot of patients with obesity. Taking great care (surgical, biochemical, and bioinformatic) to avoid environmental contaminants. We performed statistical discriminant analyses to identify specific signatures and constructed network of interactions between variables. The data showed that a specific 16SrRNA gene signature was composed of numerous bacterial families discriminating between lean versus patients with obesity and people with severe obesity. The main discriminant families were Burkholderiaceae, Yearsiniaceae, and Xanthomonadaceae, all of which were gram-negative. Interestingly, the Morganellaceae were totally absent from people without obesity while preponderant in all in patients with obesity. To generate hypotheses regarding their potential role, we inferred metabolic pathways from the 16SrRNA gene signatures. We identified several pathways associated with adenosyl-cobalamine previously described to be linked with adipose tissue development. We further identified chorismate biosynthesis, which is involved in aromatic amino-acid metabolism and could play a role in fat pad development. This innovative approach generates novel hypotheses regarding the gut to adipose tissue axis. This innovative approach generates novel hypotheses regarding the gut to adipose tissue axis in obesity and notably the potential role of tissue microbiota.

Metagenomic Analysis of Intratumoral Microbiome Linking to Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer

To assess taxonomic and functional characteristics of tumor-bearing microbiota and its association with response to neoadjuvant chemoradiation therapy (nCRT) in patients with locally advanced rectal cancer. We performed metagenomic sequencing of biopsy tumoral tissues from 73 patients with locally advanced rectal cancer before nCRT. Patients were classified into poor responders (PR) and good responders (GR) according to response to nCRT. Subsequent investigation of network alteration, key community, microbial biomarkers, and function related to nCRT responses were carried out. The network-driven analysis systematically revealed 2 co-occurring bacteria modules that exhibited opposite relationship with rectal cancer radiosensitivity. In the 2 modules, prominent alteration of global graph properties and community structure was observed between networks of PR and GR group. By quantifying changes in between-group association patterns and abundances, a total of 115 discriminative biomarker species linked to nCRT response were found, and 35 microbial variables were selected to establish the optimal randomForest classifier for nCRT response prediction. It yielded an area under the curve value of 85.5% (95% CI, 73.3%-97.8%) in the training cohort and 88.4% (95% CI, 77.5%-99.4%) in the validation cohort. In a comprehensive consideration, 5 key bacteria showed high relevance with inducing resistance to nCRT, including Streptococcus equinus, Schaalia odontolytica, Clostridium hylemonae, Blautia producta, and Pseudomonas azotoformans. One key hub including several butyrate-formation bacteria involving with driving network alteration from GR to PR indicate that microbiota-derived butyrate may also be involved in reducing the antitumor effects of nCRT, especially Coprococcus. The functional analysis of metagenome linked the nitrate and sulfate-sulfur assimilation, histidine catabolic process, and resistance to cephamycin to the reduced therapeutic response. It also linked to leucine degradation, isoleucine biosynthesis, taurine, and hypotaurine metabolism to the improved response to nCRT. Our data offer novel potential microbial factors and shared metagenome function linked to resistance to nCRT.

Seasonal Variation in Gut Microbiota of the Wild Daurian Ground Squirrel (Spermophilus dauricus): Metagenomic Insights into Seasonal Breeding.

The Spermophilus dauricus, the wild Daurian ground squirrel, is known to exhibit seasonal breeding behavior. Although the importance of gut microbiota in animal digestion, metabolism, and immunity is well-established, the correlation between gut microbiota and seasonal breeding in this species remains inadequately explored. In the present study, using metagenomic sequencing technology, the compositions and functions of the gut microbiota of wild Daurian ground squirrels in different breeding seasons were explored. The dominant gut microbial phyla were Firmicutes and Bacteroidetes. The Firmicutes were predominant in the breeding season, whereas Bacteroidetes were predominant in the non-breeding season. At the genus level, Lactobacillus accumulated during the breeding season, whereas Odoribacter and Alistipes increased during the non-breeding season. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genome) annotations indicated that genes in gut samples were highly associated with metabolic functions. The differential expression gene analysis showed that genes related to the phosphotransferase system, cysteine, and methionine metabolism were highly expressed during the breeding season, whereas the non-breeding season upregulated genes were enriched in starch and sucrose metabolism and bacterial chemotaxis pathways. In conclusion, this study could provide a reference for investigating gut microbiota in seasonal breeding animals and offer new insight into gut microbial function.

Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability

Microplastics (MPs) have emerged as widely existing global environmental concerns in terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes and their metagenomic functioning is currently uncertain. Herein, we investigated the response mechanisms of bacterial and fungal communities as well as the metagenomic functions to the addition of MPs in two soils with distinct pH and heavy metals. In this study, the acidic soil (Xintong) and the neutral soil (Huanshan) contaminated by heavy metals were incubated with Polyvinyl Chloride (PVC) MPs at ratios of 2.5% and 5% on 60 and 120 days. We aimed to evaluate the responding, assembly, and interactions of the metagenomic taxonomy and function. Results showed that only in the acidic soil, PVC MPs significantly increased soil pH and decreased CaCl2-extractable heavy metals, and also reduced bacterial alpha diversity and interaction networks. The relative proportions of Proteobacteria and Bacteroidota in bacteria, and Mortierellomycota in fungi, were increased, but Chloroflexi and Acidobacteriota in bacteria, Ascomycota and Basidiomycota in fungi, were significantly decreased by PVC MPs. Metagenomic functions related to C cycling were repressed but the nutrient cycles were enriched with PVC MPs. In conclusion, our study suggests that the addition of PVC MPs could shift soil microbial community and metagenomic functioning, as well as increasing soil pH and reduced heavy metal availability.

The faecal microbiome of Exmoor ponies shows step-wise compositional changes with increasing levels of management by humans.

Horses can suffer from gastrointestinal (GI) disease in domestic environments, often precipitated by human-led changes in management. Understanding the consequences of these changes on equine gut microbiota is key to the prevention of such disease episodes. Profile the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of management by humans, encompassing different diets; whilst controlling for age, breed and sex. Cross-sectional descriptive. Faecal samples were collected from three populations of Exmoor ponies kept under contrasting management conditions: 29 adult female ponies in groups with low management (LM) (n = 10), medium management (MM) (n = 10) and high management (HM) (n = 9) levels, based on diet, drug use, handling and exercise. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene, and functional metagenome predictions. We observed profound step-wise changes in microbiome structure in the transition from LM to MM to HM. A relatively high abundance of Proteobacteria and Tenericutes was associated with the HM group; higher abundance of Methanobacteria was observed in the LM group. The MM group had intermediate levels of these taxa and exhibited high 'within group' variation in alpha diversity. Functional predictions revealed increased amino acid and lipid metabolism in HM; energy metabolism in LM and carbohydrate metabolism and immune/metabolic disease pathways in MM. Low group sizes, incomplete knowledge of bacterial genomes in equine gut microbiota and it was not possible to assess the relative impact of diet, drug use, handling and exercise on the microbiome as variables were confounded. Human-led management factors had profound step-wise effects on faecal microbial composition. Based on functional metagenome predictions, we hypothesise that dietary differences between groups were the major driver of observed differences.

Promotion of longitudinal bone growth by the intake of oat and green onion root water extracts in weaning rats through stimulating growth hormone secretion and elevating gut microbiota related to nervous system-related pathway

We determined whether oral oat and green onion water extracts (GOO) supplementation could stimulate longitudinal bone growth in weaning rats. Fistuloside A, B, and C in the green onions and 26-desglucoavenacoside A and B and avenacoside A in the oats lowered the binding energy of growth differentiation factor-5 (GDF5) and insulin-like growth factor-1 receptor (IGF1R). After a 4-week treatment, serum growth hormone (GH) and osteoprotegerin concentrations in the High-GOO group (500 mg/kg body weight) were similar to those of the Positive-control. The femur and tibia lengths promoting the proliferative and hypertrophic zones of the growth plate in the High-GOO were also similar to Positive-control. Along with increasing serum propionate and butyrate concentrations, cecal bacteria in the High-GOO were higher in virus infection, steroid and sesquiterpenoid biosynthesis, and nervous system-related pathways than the Control in the metagenome function. It suggested that gut bacteria potentially enhanced bone growth by improving immunity and neurological activity. In conclusion, GOO increased leg length by enhancing the proliferation of the growth plate as much as GH treatment by preventing gut dysbiosis.

Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes.

T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial composition, co-abundance network, and metagenome function in US adults with T2DM compared to healthy adults based on enterotypes. We analyzed 1911 fecal bacterial files of 1039 T2DM and 872 healthy US adults from the Human Microbiome Projects. Operational taxonomic units were obtained after filtering and cleaning the files using Qiime2 tools. Machine learning and network analysis identified primary bacteria and their interactions influencing T2DM incidence, clustered into enterotypes, Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). ET-B showed higher T2DM incidence. Alpha-diversity was significantly lower in T2DM in ET-L and ET-P (p < 0.0001), but not in ET-B. Beta-diversity revealed a distinct separation between T2DM and healthy groups across all enterotypes (p < 0.0001). The XGBoost model exhibited high accuracy and sensitivity. Enterocloster bolteae, Facalicatena fissicatena, Clostridium symbiosum, and Facalibacterium prausnitizii were more abundant in the T2DM group than in the healthy group. Bacteroides koreensis, Oscillibacter ruminantium, Bacteroides uniformis, and Blautia wexlerae were lower in the T2DM than in the healthy group regardless of the enterotypes in the XGBoost model (p < 0.0001). However, the patterns of microbial interactions varied among different enterotypes affecting T2DM risk. The interaction between fecal bacteria was more tightly regulated in the ET-L than in the ET-B and ET-P groups (p < 0.001). Metagenomic analysis revealed an inverse association between bacteria abundance in T2DM, energy utility, butanoate and propanoate metabolism, and the insulin signaling pathway (p < 0.0001). In conclusion, fecal bacteria play a role in T2DM pathogenesis, particularly within different enterotypes, providing valuable insights into the link between gut microbiota and T2DM in the US population.

Microbiological Characterization of the Biofilms Colonizing Bioplastics in Natural Marine Conditions: A Comparison between PHBV and PLA.

Biodegradable polymers offer a potential solution to marine pollution caused by plastic waste. The marine biofilms that formed on the surfaces of poly(lactide acid) (PLA) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were studied. Bioplastics were exposed for 6 months to marine conditions in the Mediterranean Sea, and the biofilms that formed on their surfaces were assessed. The presence of specific PLA and PHBV degraders was also studied. PHBV showed extensive areas with microbial accumulations and this led to higher microbial surface densities than PLA (4.75 vs. 5.16 log CFU/cm2). Both polymers' surfaces showed a wide variety of microbial structures, including bacteria, fungi, unicellular algae and choanoflagellates. A high bacterial diversity was observed, with differences between the two polymers, particularly at the phylum level, with over 70% of bacteria affiliated to three phyla. Differences in metagenome functions were also detected, revealing a higher presence of proteins involved in PHBV biodegradation in PHBV biofilms. Four bacterial isolates belonging to the Proteobacteria class were identified as PHBV degraders, demonstrating the presence of species involved in the biodegradation of this polymer in seawater. No PLA degraders were detected, confirming its low biodegradability in marine environments. This was a pilot study to establish a baseline for further studies aimed at comprehending the marine biodegradation of biopolymers.

Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata.

Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.