Predictive Functional Profiling Research Articles

The Effect of Clostridium butyricum on Gut Microbial Changes and Functional Profiles of Metabolism in High-fat Diet-fed Rats Depending on Age and Sex.

A high-fat diet (HFD) causes dysbiosis and promotes inflammatory responses in the colon. This study aims to evaluate the effects of Clostridium butyricum on HFD-induced gut microbial changes in rats. Six-week-old Fischer-344 rats with both sexes were given a control or HFD during 8 weeks, and 1-to-100-fold diluted Clostridium butyricum were administered by gavage. Fecal microbiota analyses were conducted using 16S ribosomal RNA metagenomic sequencing and predictive functional profiling of microbial communities in metabolism. A significant increase in Ruminococcaceae and Lachnospiraceae, which are butyric acid-producing bacterial families, was observed in the probiotics groups depending on sex. In contrast, Akkermansia muciniphila, which increased through a HFD regardless of sex, and decreased in the probiotics groups. A. muciniphila positively correlated with Claudin-1 expression in males (P < 0.001) and negatively correlated with the expression of Claudin-2 (P = 0.042), IL-1β (P = 0.037), and IL-6 (P = 0.044) in females. In terms of functional analyses, a HFD decreased the relative abundances of M00131 (carbohydrate metabolism module), M00579, and M00608 (energy metabolism), and increased those of M00307 (carbohydrate metabolism), regardless of sex. However, these changes recovered especially in male C. butyricum groups. Furthermore, M00131, M00579, and M00608 showed a positive correlation and M00307 showed a negative correlation with the relative abundance of A. muciniphila (P < 0.001). The beneficial effects of C. butyricum on HFD-induced gut dysbiosis in young male rats originate from the functional profiles of carbohydrate and energy metabolism.

Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices.

Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.

Lactic acid bacteria in some Indian fermented foods and their predictive functional profiles

Lactic acid bacteria in some Indian fermented foods and their predictive functional profiles

Urine microbes and predictive metagenomic profiles associate with abnormalities in sperm parameters: implications for male subfertility

To explore the taxonomic and predicted functional relationship between the urine microbiome and alterations of semen analysis (SA) parameters. Cross-sectional study. Academic medical center. Men presenting for fertility evaluation or men presenting for vasectomy consultation with proven biological paternity were recruited and stratified on the basis of alterations, or lack thereof, in SA parameters. Changes in the functional and taxonomic urine microbiome profiles of participants with or without alterations in SA parameters. Seventy-three participants were included in our study. Men with abnormal sperm motility (N = 27) showed a nearly 50-fold higher abundance of Dialister micraerophilus compared with those with normal sperm motility (N = 46). This relationship persisted on canonical correlational analysis (r = 0.439). Men with abnormal sperm concentration (N = 20) showed a lower abundance of Enterococcus faecalis and Staphylococcus aureus, compared with those with normal sperm concentration (N = 53). The urine of participants with impaired sperm motility demonstrated dramatic differences in predictive functional profiles in pathways involved in oxidation-reduction balance and cell longevity. Our findings underscore differences in the urinary microbiome and abnormalities in semen parameters, especially sperm motility. By incorporating predictive functional profiling, we also highlight possible mechanisms that may drive the observed differences in sperm parameters.

Temporal patterns of bacterial communities in the Billings Reservoir system

In this study, high-throughput sequencing of 16S rRNA amplicons and predictive PICRUSt functional profiles were used to perform a comprehensive analysis of the temporal bacterial distribution and metabolic functions of 19 bimonthly samples collected from July 2019 to January 2020 in the surface water of Billings Reservoir, São Paulo. The results revealed that most of the bacterial 16S rRNA gene sequences belonged to Cyanobacteria and Proteobacteria, which accounted for more than 58% of the total bacterial abundance. Species richness and evenness indices were highest in surface water from summer samples (January 2020), followed by winter (July 2019) and spring samples (September and November 2019). Results also showed that the highest concentrations of sulfate (SO4–2), phosphate (P), ammonia (NH3), and nitrate (NO3-) were detected in November 2019 and January 2020 compared with samples collected in July and September 2019 (P < 0.05). Principal component analysis suggests that physicochemical factors such as pH, DO, temperature, and NH3 are the most important environmental factors influencing spatial and temporal variations in the community structure of bacterioplankton. At the genus level, 18.3% and 9.9% of OTUs in the July and September 2019 samples, respectively, were assigned to Planktothrix, while 14.4% and 20% of OTUs in the November 2019 and January 2020 samples, respectively, were assigned to Microcystis. In addition, PICRUSt metabolic analysis revealed increasing enrichment of genes in surface water associated with multiple metabolic processes rather than a single regulatory mechanism. This is the first study to examine the temporal dynamics of bacterioplankton and its function in Billings Reservoir during the winter, spring, and summer seasons. The study provides comprehensive reference information on the effects of an artificial habitat on the bacterioplankton community that can be used to interpret the results of studies to evaluate and set appropriate treatment targets.

Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures.

Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2℃ in 3% w/v crude oil), A (25 ± 2℃ in 1% w/v crude oil), H (25 ± 2℃ in 3% w/v crude oil), and X (45 ± 2℃ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.

Metagenomics and metagenome-assembled genomes analysis of sieng, an ethnic fermented soybean food of Cambodia

Sieng is an ethnic fermented soybean food of Cambodia. No information on microbial community structures and their roles in health benefits of sieng is available till date. Hence, we aimed to profile the microbial community structures, to infer predictive functionalities and to recover the high-quality metagenome-assembled genomes (MAGs). Bacillus subtilis was the most abundant species in sieng, followed by Tetragenococcus halophilus, Enterococcus sp., Brevibacillus borstelensis, B. cereus, B. glycinifermentans, Halanaerobium praevalens, Mammaliicoccus sciuri, Staphylococcus gallinarum, Enterococcus faecium, B. cytotoxicus, Aneurinibacillus migulanus, B. thermoamylovorans, Paenibacillus dendritiformis and B. velezensis. Predictive functional profiles of sieng revealed several KEGG pathways and detection of CRISPR-Cas proteins. Six high-quality MAGs were recovered and identified as Bacillus subtilis, B. velezensis, B. glycinifermentans, B. borstelensis, B. thermoamylovorans and Ligilactobacillus acidipiscis. Genome annotation of recovered genomes showed biomarker genes for encoding several functional properties. Comparative analysis of previously reported microbiota in similar Asian sticky fermented soybean foods of other countries viz. Kinema of India, Nepal and Bhutan, pe poke of Myanmar and cheonggukjang of Korea with sieng was also studied. The PCoA plot showed a discrete variation between sieng and metagenomes of other similar fermented soybean foods, based on species level. However, sieng metagenome recorded the presence of halophilic bacterial species in higher abundance unlike other fermented soybean products. The present work is the first report on microbial community structure, and metagenome-assembled genomes of sieng.

Cold isostatic pressing-study on methane production and microbial communities in anaerobic digestion of wheat straw with high-solids

In this study, the effect of cold isostatic pressing (CIP) pretreatment on the physicochemical properties and subsequent anaerobic digestion (AD) performance of wheat straw (WS) was explored, which did not have additional chemical reagent over the whole process. The WS was subjected to CIP pretreatment by pressures from 350 to 700 MPa, respectively, while AD was carried out at mesophilic temperature with total solids (TS) 7% and 14%. The mapping indicated that the CIP pretreatment promoted the hydrolysis of WS by destroying the dense structure. The CIP pretreatment changed pH and volatile fatty acids (VFAs) in the AD system. Compared with the control group, the cumulative methane production of CIP pretreatment group with TS 14% increased by 22.07%–56.18%. The acetic acid concentration peaked on 4th day and 14th day with 3943.23 mg/L and 3815.21 mg/L, respectively, in H600, and propionic acid concentration also reached two peaks at the same time with 2014.92 mg/L and 2405.20 mg/L, respectively. It was also observed that the CIP pretreatment maintained the pH in the range of 6.44–7.40, maintaining the stability of the overall system. It was also found that CIP pretreatment increased 9 species of hydrolysis and acidogenic bacteria, and methanogen Methanosarcina, thereby facilitating the hydrolysis and methanogenic stages. Predictive functional profiling comfirmed that CIP pretreatment could promote glycolysis/gluconeogenesis, fatty acid metabolism, and fatty acid degradation, whose relative abundance increased from 1.10% to 1.13%, 0.60%–0.62%, and 0.19%–0.23%. Methanogenic capacity of the system was improved because of CIP pretreatment enhancing the accessibility of microorganisms by disrupting the microstructure of WS. The energy conversion analysis showed that this method without chemical reagent addition is feasible for high-solids anaerobic digestion.

The Protective Effect of Roseburia faecis Against Repeated Water Avoidance Stress-induced Irritable Bowel Syndrome in a Wister Rat Model.

Roseburia faecis, a butyrate-producing, gram-positive anaerobic bacterium, was evaluated for its usefulness against repeated water avoidance stress (WAS)-induced irritable bowel syndrome (IBS) in a rat model, and the underlying mechanism was explored. We divided the subjects into three groups: one without stress exposure, another subjected to daily 1-hour WAS for 10 days, and a third exposed to the same WAS regimen while also receiving two different R. faecis strains (BBH024 or R22-12-24) via oral gavage for the same 10-day duration. Fecal pellet output (FPO), a toluidine blue assay for mast cell infiltration, and fecal microbiota analyses were conducted using 16S rRNA metagenomic sequencing. Predictive functional profiling of microbial communities in metabolism was also conducted. FPO and colonic mucosal mast cell counts were significantly higher in the WAS group than in the control group (male, P = 0.004; female, P = 0.027). The administration of both BBH024 (male, P = 0.015; female, P = 0.022) and R22-12-24 (male, P = 0.003; female, P = 0.040) significantly reduced FPO. Submucosal mast cell infiltration in the colon showed a similar pattern in males. In case of fecal microbiota, the WAS with R. faecis group showed increased abundance of the Roseburia genus compared to WAS alone. Moreover, the expression of a gene encoding a D-methionine transport system substrate-binding protein was significantly elevated in the WAS with R. faecis group compared to that in the WAS (male, P = 0.028; female, P = 0.025) group. These results indicate that R. faecis is a useful probiotic for treating IBS and colonic microinflammation.

Metataxonomic Characterization of Enriched Consortia Derived from Oil Spill-Contaminated Sites in Guimaras, Philippines, Reveals Major Role of Klebsiella sp. in Hydrocarbon Degradation.

Oil spills are major anthropogenic disasters that cause serious harm to marine environments. In the Philippines, traditional methods of rehabilitating oil-polluted areas were proven to be less efficient and cause further damage to the environment. Microbial degradation has poised itself to be a promising alternative to those traditional methods in remediating oil spills. Hence, the present study aimed to enrich and characterize hydrocarbon-degrading microbial consortia from oil-contaminated regions in Guimaras Island for potential use in bioremediation. A total of 75 soil samples were obtained and used as inoculum for the enrichment for hydrocarbon degraders. Afterwards, 32 consortia were recovered and subjected to the 2,6-DCPIP assay for biodegradation ability on four types of hydrocarbons: diesel, xylene, hexane, and hexadecane. The consortia that obtained the highest percent degradation for each of the four hydrocarbons were "B2" (92.34% diesel degraded), "A5" (85.55% hexadecane degraded), "B1" (74.33% hexane degraded), and "B7" (63.38% xylene degraded). Illumina MiSeq 16S rRNA gene amplicon sequencing revealed that the dominant phyla in all consortia are Pseudomonadota (previously Proteobacteria), followed by Bacillota (previously Firmicutes). Overall, the amplicon sequence variants (ASVs) retrieved were mainly from the Gammaproteobacteria class, in which many hydrocarbon-degrading bacteria are found. Predictive functional profiling of the consortium showed the presence of genes involved in the degradation of recalcitrant hydrocarbon pollutants. Fatty acid metabolism, which includes alkB (alkane-1-monooxygenase) and genes for beta oxidation, was inferred to be the most abundant amongst all hydrocarbon degradation pathways. Klebsiella sp. is the predominant ASV in all the sequenced consortia as well as the major contributor of hydrocarbon degradation genes. The findings of the study can serve as groundwork for the development of hydrocarbon-degrading bacterial consortia for the bioremediation of oil spill-affected areas in the Philippines. Likewise, this paper provides a basis for further investigation into the role of Klebsiella sp. in the bioremediation of hydrocarbon pollutants.

High-fiber diet and rope-skipping benefit cardiometabolic health and modulate gut microbiota in young adults: A randomized controlled trial

Previous studies have shown that high intake of dietary fiber (DF) and efficient levels of physical activity are beneficial for cardiometabolic health in middle-aged and elderly populations with cardiometabolic disease. However, evidence from young adults with low cardiometabolic risk is lacking. This study aimed to investigate the effects of various interventions including a high-fiber (HF) diet and the rope-skipping (RS) exercise on cardiometabolic risk factors (CRFs) and the composition of the gut microbiota in young adults. A 12-week parallel-designed randomized controlled trial was conducted in undergraduates (n = 96), who were randomly assigned to the HF group (≥20 g/d DF), the RS group (2000 jumps/week), and the control (CON) group. Among the 84 people who completed the trial, measurements of anthropometric characteristics, biochemical parameters, and gut microbiota were taken at the beginning and end of the intervention. After the intervention, the RS exercise led to a significant decrease in the heart rate and triglyceride levels compared to the CON group (all P < 0.05), but there was no significant difference in CRFs between the HF and CON groups. When compared to baseline, the 12-week HF diet intervention resulted in an increase in fat-free mass, and a decrease in the percentage of body fat and waist circumference (all P < 0.05). With regard to gut microbiota alterations after intervention, we found that compared with the CON group, the relative abundance of Lactobacillus decreased significantly in both the HF group and the RS group, Muribaculaceae decreased in the RS group, and Eubacterium_coprostanoligenes_group decreased in the HF group (all P < 0.05). Finally, shifts in 7 metabolic pathways were detected in the RS group using predictive functional profiling, while only one pathway was altered in the HF group (all P < 0.05). In conclusion, the RS exercise improved body composition compared to the CON group in young adults, while the HF diet just enhanced CRFs in contrast to baseline. Furthermore, both RS and HF interventions altered Lactobacillus and various other gut microbiota. The results indicated that the HF diet and RS exercise could partly benefit cardiometabolic health and modulate gut microbiota in young adults. Trial registration: ClinicalTrials.gov, NCT04834687.

The effect of single dose albendazole (400 mg) treatment on the human gut microbiome of hookworm-infected Ghanaian individuals

Microbes play a key role in human gut homeostasis, metabolic, immunologic and physiopathology of the body. A longitudinal study conducted during 2018–2021 in the Kintampo North Municipality in Ghana demonstrated low hookworm infection cure rates following treatment with a single dose of 400 mg albendazole in some communities. To investigate associations between hookworm infection and the gut microbiome, we examined stool samples from consented participants who were either cured or remained infected after treatment. At each time point, stool was collected prior to and 10–14 days after albendazole treatment. We used 16S rRNA amplicon sequencing of DNA extracted from stool samples to investigate the composition and diversity of the gut microbiota and to identify potential microbial biomarkers associated with treatment outcomes. Hookworm infection was associated with increased species richness (p = 0.0093). Among treated individuals, there was also a significant variation in microbiota composition at 10–14 days following single-dose albendazole treatment. Individuals cured of hookworm infection after treatment showed a significant reduction in microbiota composition when compared to their pre-treatment state (ANOSIM; p = 0.02), whilst individuals who failed to clear the infection showed no change in microbiota composition (ANOSIM; p = 0.35). Uninfected individuals and those who were successfully treated were similar in their microbial composition and structure. We also found that the abundance of Clostridia spp. was increased in infected individuals pre- or post-treatment. Predictive functional profiling revealed the enrichment of two pyruvate ferredoxin oxidoreductase subunit pathways in individuals who remained infected after treatment (p < 0.05), alluding to an upturn of strictly anaerobic commensal bacteria such as Clostridia spp. This study suggests a relationship between human gut microbiome dysbiosis and albendazole therapy outcomes of hookworm infection. Future studies will further characterize specific biomarkers identified within this study to establish their potential for assessment of pharmacological responses to anthelminthic therapies, as well as explore the possibility of using probiotic supplementation as an adjunct treatment to increase albendazole effectiveness against hookworm.

Rumen microbiome response to sustained release mineral bolus supplement with low- and high-quality forages

IntroductionLimited forage quantity and quality are challenges faced in livestock production systems in semi-arid rangelands of the western United States, particularly when livestock face stressors such as cold weather or have increased nutritional requirements such as during pregnancy and lactation. To meet livestock nutrient requirements, producers frequently provide supplemental nutrition, however there is limited knowledge regarding the effects of these practices on the rumen microbiome in these environments.MethodsA study was conducted to evaluate changes in the rumen microbiome in response to high- and low- quality forage with sustained release mineral boluses. The study consisted of 16 ruminally-cannulated 2–3-year-old black angus cows fed high quality grass alfalfa hay or low-quality grass hay with a 90 or 180 day sustained release mineral bolus. Rumen samples were collected pre-feeding and 8 hours post feeding and bacterial 16S rRNA gene amplicons were sequenced from the rumen fluid.ResultsAlpha diversity as measured by Shannon’s diversity index decreased significantly over time (p&amp;lt;0.01) and averaged 5.6 pre-feeding and 5.4 post- feeding and was not significantly different between high- and low-quality forages or between mineral bolus types (p&amp;gt;0.05). Principal coordinates analysis (PCoA) of the Bray-Curtis dissimilarity matrix showed distinct grouping by feed quality and time but not by mineral bolus type. Bacteroidetes and Firmicutes were the dominant phyla in all treatments and significant increases (p&amp;lt;0.05) in the relative abundance of the family Lachnospiraceae and the genus Prevotella were observed in high quality forage diets. Rumen VFA and NH3-N concentrations were also strongly associated with the high-quality forage diet. Predictive functional profiling indicated that functions associated with methanogenesis were negatively correlated with feed quality.DiscussionThe results of this study suggest that mineral bolus type is unlikely to affect rumen bacterial community structure or function while forage quality can significantly alter community structure and predicted functions associated with methanogenesis and VFA production.

The contribution shift of ammonia-oxidizing archaea and bacteria to ammoxidation under Ag-NPs/SWCNTs/PS-NPs stressors in constructed wetlands

Ammonia-oxidizing microorganisms (AOMs, archaea (AOA) and bacteria (AOB)) are primarily responsible for the ammoxidation in constructed wetlands (CWs). However, little is known about evaluating the response of AOA and AOB to engineered nanomaterials (ENMs) and quantifying the shift of their contribution to ammoxidation. Herein, we operated a series of CWs exposing to silver nanoparticles (Ag-NPs), single-walled carbon nanotubes (SWCNTs), and polystyrene nano-sized plastics (PS-NPs) with the wastewater-accumulating concentration of ENMs for 180 days. The results showed that the abundance of AOA amoA gene in situ was far lower than that of AOB, while the abundance ratio of AOA to AOB increased by 15 folds after 180-day experiment. Using DNA stable isotope probing (DNA-SIP) experiment, we found that the active AOB microbiota varied substantially but the AOA was more stable across different groups. Furthermore, the co-occurrence analysis proved that ENMs stress increased the negative coexistence pattern of AOA and AOB; predictive functional profiling showed that the ENMs enhanced the functional advantage of AOA by inhibiting AOB (mainly hydroxylamine oxidation process). Finally, the contribution of AOA increased under exposing to SWCNTs (18.35%), PS-NPs (24.92%), and Ag-NPs (32.14%) compared with control group (0.03%) for 180 days. Despite this, AOB was still the primary executant of ammoxidation in CWs. Overall, in our study, the differences in activities and contributions of AOMs were quantified in CWs, and a significantly negative coexistence relationship between AOA and AOB was revealed when exposed to emerging nanomaterials.

Starvation alters gut microbiome and mitigates off-flavors in largemouth bass (Micropterus salmoides).

The present study aimed to investigate the response of intestinal microbiota during 3weeks' starvation of largemouth bass (Micropterus salmoides), an economically important freshwater fish, using 16S rRNA gene amplicon sequencing and PICRUSt2 predictive functional profiling. Overall, the microbiota was mainly represented by Mycoplasma, Pseudomonas, Acinetobacter, and Microbacterium in the initial group. This pattern contrasted with that of Cetobacterium and Aeromonas, which were major representative genera in the starved group. Significant differences in the richness and composition of intestinal microbial community induced by starvation were observed. Notably, earthy-musty off-flavor compounds (geosmin and 2-methylisoborneol) were significantly decreased during starvation, which were significantly correlated with the abundance of certain actinobacterial taxa, namely, Microbacterium and Nocardioides. Additionally, the functional pathways involved in synthesis of off-flavor compounds, protein digestion, fatty acid degradation, and biosynthesis of cofactors greatly decreased with starvation, indicating that microbiota modulated the specific metabolic pathway to adapt to food deprivation. These results emphasize that starvation can modulate diversity, community structure, and functions of the intestinal microbiota and mitigate the off-flavors, which has important implications for strategies to eliminate off-flavor odorants through the application of probiotics to manipulate the gut microbiome and ultimately enhance flesh quality of freshwater fish.

Diversity and assembly of active bacteria and their potential function along soil aggregates in a paddy field

Numerous studies have found that soil microbiomes differ at the aggregate level indicating they provide spatially heterogeneous habitats for microbial communities to develop. However, an understanding of the assembly processes and the functional profile of microbes at the aggregate level remain largely rudimentary, particularly for those active members in soil aggregates. In this study, we investigated the diversity, co-occurrence network, assembly process and predictive functional profile of active bacteria in aggregates of different sizes using H218O-based DNA stable isotope probing (SIP) and 16S rRNA gene sequencing. Most of the bacterial reads were active with 91 % of total reads incorporating labelled water during the incubation. The active microbial community belonged mostly of Proteobacteria and Actinobacteria, with a relative abundance of 55.32 % and 28.12 %, respectively. Assembly processes of the active bacteria were more stochastic than total bacteria, while the assembly processes of total bacteria were more influenced by deterministic processes. Furthermore, many functional profiles such as environmental information processing increased in active bacteria (19.39 %) compared to total bacteria (11.22 %). After incubation, the diversity and relative abundance of active bacteria of certain phyla increased, such as Proteobacteria (50.70 % to 59.95 %), Gemmatimonadetes (2.63 % to 4.11 %), and Bacteroidetes (1.50 % to 2.84 %). In small macroaggregates (SMA: 0.25-2 mm), the active bacterial community and its assembly processes differed from that of other soil aggregates (MA: microaggregates, <0.25 mm; LMA: large macroaggregates, 2-4 mm). For functional profiles, the relative abundance of important functions, such as amino acid metabolism, signal transduction and cell motility, increased with incubation days and/or in SMA compared to other aggregates. This study provides robust evidence that the community of active bacteria and its assembly processes in soil aggregates differed from total bacteria, and suggests the importance of dominant active bacteria (such as Proteobacteria) for the predicted functional profiles in the soil ecosystem.

Adaptation of anammox consortia in microbial fuel cell to low temperature: Microbial community and predictive functional profiling

The purpose of this study was to explore the tolerance mechanism of anammox consortia in microbial fuel cell (MFC) system at low temperature. Data showed that nearly 80 % total nitrogen removal was achieved after the temperature decreased from 30 °C to 15 °C. The nitrogenremovalrate (NRR) of the system was decreased by 26.3 %, from 0.441 kgN·m−3·d−1 at 30 °C to 0.325 kgN·m−3·d−1 at 15 °C. Isotope experiment in 15NH4+-containing reactor found that much more 29N2 were produced than 30N2, confirming that anammox was the main 15NH4+ removal pathway and electrochemical oxidation participate in this process. High throughput sequencing analysis indicated the low temperature stimulated the enrichment of heterotrophic bacteria, such as Comamonadaceae and Rhodobacteraceae. While the relative abundance of Candidatus Brocadia, typical anammox bacteria, decreased significantly. Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis showed that the low temperature induced a more efficient expression in synthesis of unsaturated fatty acids (UFAs) and ABC membrane transports. This study indicates that anammox consortia are likely to maintain high nitrogen removal performance of MFC system by changing the proportion of membrane composition and EPS exportation.

Bioorganic fertilizer promotes pakchoi growth and shapes the soil microbial structure.

As a functional probiotic, Bacillus subtilis can promote crop growth and improve nutrient utilization by various mechanisms, so it has been made into bioorganic fertilizer as a replacement for chemical fertilizer. However, the effects of B. subtilis bioorganic fertilizer application on the yield and quality of commercial crops of Brassica chinensis L., the soil physicochemical properties and the microflora have not been clarified. In this study, pot experiments were conducted using Brassica chinensis L. plants with four fertilization treatments: control without fertilization (CK), chemical fertilizer (CF), organic fertilizer (OF), and bioorganic fertilizer containing B. subtilis (BF). After 30 days of pot experiment, the results showed that BF efficiently improved plant height and biomass (1.20- and 1.93-fold, respectively); as well as significantly increasing soil available potassium and pH value. Using high-throughput sequencing, we examined the bacterial and fungal communities in the soil, and found that their diversity was remarkablely reduced in the BF treatment compared to CK group. A principal coordinate analysis also showed a clear separation of bacterial and fungal communities in the BF and CK groups. After application of B. subtilis bioorganic fertilizer, some beneficial bacteria (such as Bacillus and Ammoniphilus) and fungi (Trichoderma and Mortierella) were enriched. A network analysis indicated that bacteria were the dominant soil microbes and the presence of B. subtilis stimulated the colonization of beneficial microbial communities. In addition, predictive functional profiling demonstrated that the application of bioorganic fertilizer enhanced the function of mineral element metabolism and absorption and increased the relative abundance of saprotrophs. Overall, the application of bioorganic fertilizer effectively changed the soil microflora, improved the soil available potassium and pH value, and boosted the yield of Brassica chinensis L. This work has valuable implications for promoting the safe planting of facility vegetables and the sustainable development of green agriculture.

Expression and Predictive Functional Profiles of MicroRNAs Data in Vascularized Composite Allotransplantation Acute Rejection.

This study aimed to investigate the mechanisms of acute rejection for vascularized composite allotransplantation (VCA) using microRNAs (miRNAs) differential expression in a VCA animal model. Brown Norway rats were used as transplant donors and Lewis rats as VCA receptors. The changes were divided into different stages before and after transplantation in Lewis rats, and all appearance changes were recorded. Also, histological evaluations were performed on all recipients, and the expression of microRNAs was analyzed when acute immune rejection occurred. Then, we used GO and KEGG Pathway enrichment analyses to predict miRNA targets. Finally, differentially expressed miRNAs were detected by RT-qPCR. Compared to pre-operation, 22 miRNAs were differentially expressed after operations. Among them, nine were upregulated, and 13 were downregulated in skin tissues. The RT-qPCR results revealed that rno-miR-340-5p and rno-miR-21-5p were significantly upregulated and enriched in the PI3K-Akt signaling pathway. Moreover, rno-miR-145-5p and rno-miR-195-5p were significantly downregulated, and most of their target genes were enriched in the Hippo signaling pathway. The histological evaluations showed that, after VCA, the skin tissue presented severe acute rejection. The miRNAs rno-miR-340-5p, rno-miR-21-5p, rno-miR-145-5p, and rno-miR-195-5p were significantly regulated during VCA acute rejection, when the four miRNAs analyses were done on skin biopsies. These miRNAs might be potential biomarkers for objective, early, and minimally invasive rejection diagnosis.

Shifts of bacterial community and predictive functional profiling of denitrifying phosphorus removal – Partial nitrification – Anammox three-stage nitrogen and phosphorus removal before and after coupling for treating simulated wastewater with low C/N

The feasibility of simultaneous denitrification phosphorus removal (DPR) partial nitrification (PN) and anammox (AMX) process were investigated in a coupling three-stage sequencing batch reactors (SBR) system for treating municipal sewage. Functional bacteria were pre-cultured and then coupled for low matrix simulated municipal wastewater treatment (50 mgN·L−1, 10 mgP·L−1 and 200 mgCOD·L−1). The total nitrogen (TN) removal efficiency of 79.94%, a phosphorus removal efficiency of 93.62%, and a chemical oxygen demand (COD) removal efficiency of 92.34% were achieved during coupling operation. The periodic experiment results showed that the contributions of anoxic and aerobic phosphorus uptake were 65.52% and 34.48%, respectively. The simultaneous nitrification and denitrification occurred in the PN reactor. Further microbial community illustrated that the coupling operation changed the structure of bacteria in three SBRs. The main functional groups were AOB Nitrosomonas, anammox bacteria Candidatus Brocadia, DPAO Acinetobacter and PAO norank_f_Caldilineaceae in coupling progress. Network-based analyses and functional genes forecast based onKEGGdatabase revealed that the microbial community in each reactor adopted different regulation pathways to improve resistance to system coupling operation. The results of this study provide the basis for understanding the process variations from the pre-culture to coupling operation for three-sludge DPR-PN-AMX municipal wastewater treatment process, which is important to quick start-up and efficient operation of coupling process.