Changes In Microbial Composition Research Articles

Fire modifies plant-soil feedbacks.

Although plant-soil feedbacks (interactions between plants and soils, often mediated by soil microbes, abbreviated as PSFs) are widely known to influence patterns of plant diversity at local and landscape scales, these interactions are rarely examined in the context of important environmental factors. Resolving the roles of environmental factors is important because the environmental context may alter PSF patterns by modifying the strength or even direction of PSFs for certain species. One important environmental factor that is increasing in scale and frequency with climate change is fire, though the influence of fire on PSFs remains essentially unexamined. By changing microbial community composition, fire may alter the microbes available to colonize the roots of plants and thus seedling growth post-fire. This has potential to change the strength and/or direction of PSFs, depending on how such changes in microbial community composition occur and the plant species with which the microbes interact. We examined how a recent fire altered PSFs of two leguminous, nitrogen-fixing tree species in Hawai'i. For both species, growing in conspecific soil resulted in higher plant performance (as measured by biomass production) than growing in heterospecific soil. This pattern was mediated by nodule formation, an important process for growth for legume species. Fire weakened PSFs for these species and therefore pairwise PSFs, which were significant in unburned soils, but were nonsignificant in burned soils. Theory suggests that positive PSFs such as those found in unburned sites would reinforce the dominance of species where they are locally dominant. The change in pairwise PSFs with burn status shows PSF-mediated dominance might diminish after fire. Our results demonstrate that fire can modify PSFs by weakening the legume-rhizobia symbiosis, which may alter local competitive dynamics between two canopy dominant tree species. These findings illustrate the importance of considering environmental context when evaluating the role of PSFs for plants.

Composition and functional profiles of human faecal microbiota fermenting plant-based food particles are related to water-holding capacity more than particle size

Particle size is regarded as an important characteristic of plant-based foods in terms of digestion and fermentation. However, it is unclear to what extent the physico-chemical characteristics of different particle sizes affect microbial composition and functionality. In this study, two different particle sizes for sorghum, wheat grain, oat bran, apple, and carrot were fermented in vitro. Following fermentation, DNA was extracted and underwent 16S gene sequencing, followed by the profiling of microbial composition and predicted functions. Associations were analysed between particle size, water-holding capacity (WHC), pectin content, microbial composition and function, and in vitro gas kinetics and fermentation end-products. WHC was driven by the presence and content of pectin, and was strongly associated with both the microbial composition, and fermentation outcomes. For example, of 39 genera with a relative abundance >0.5%, the abundance of 25 genera were significantly (P < 0.05) correlated to WHC across all samples. Within the low pectin content cereal samples, when these were analysed independently of the apple and carrot samples, WHC was also associated with fermentation outcomes. For cereal and apple samples, size reduction did not lead to obvious microbial composition and functional profile changes, possibly due to the general microbial capability to degrade starch present in cereal and comparable pectin contents in apple for different sizes. However, for different sizes of carrot, the microbial composition and functional profile alterations were related to the pectin contents. Overall, the physico-chemical characteristics, such as WHC, and both pectin and starch content are related to composition and functional profiles of human faecal microbiota following in vitro fermentation.

The protective effects of Levilactobacillus brevis FZU0713 on lipid metabolism and intestinal microbiota in hyperlipidemic rats

Levilactobacillus brevis FZU0713, a potential probiotic previously isolated from the traditional brewing process of Hongqu rice wine, may have the beneficial effects on improving lipid metabolism. This study aimed to evaluate the in vivo protective effects and possible mechanism of L. brevis FZU0713 on the disturbance of lipid metabolism in hyperlipidemic rats fed a high-fat diet (HFD). Results showed that oral administration of L. brevis FZU0713 could significantly inhibit obesity, ameliorate the lipid metabolism disorder, including serum/liver biochemical parameters and hepatic oxidative stress in HFD-fed rats. Histopathological result also indicated that dietary intervention of L. brevis FZU0713 could reduce the accumulation of lipid droplets in liver induced by 8 weeks HFD feeding. Furthermore, L. brevis FZU0713 intervention significantly increased the fecal levels of short-chain fatty acids (SCFAs, including acetate, propionate, butyrate, isobutyrate, valerate and isovalerate) in HFD-fed rats, which may be closely related to the changes of intestinal microbial composition and metabolic function. Intestinal microbiota profiling by 16S rRNA gene sequencing revealed that L. brevis FZU0713 intervention significantly altered the relative abundance of Coprococcus, Butyricicoccus, Intestinimonas, Lachnospiraceae FCS020 group, Ruminococcaceae_NK4A214 group, Ruminococcaceae_UCG-005 and UCG-014 at genus levels. Based on Spearman's rank correlation coefficient, serum and liver lipid metabolism related biochemical parameters were positively correlated with genera Ruminococcus, Pediococcus and Lachnospiraceae, but negatively correlated with genera Pseudoflavonifractor, Butyricicoccus and Intestinimonas. Furthermore, liver metabolomics analysis demonstrated that L. brevis FZU0713 had a significant regulatory effect on the composition of liver metabolites in hyperlipidemic rats, especially the levels of some important biomarkers involved in the metabolic pathways of arachidonic acid metabolism, primary bile acid biosynthesis, amino sugar and nucleotide sugar metabolism, taurine and hypotaurine metabolism, biosynthesis of unsaturated fatty acid, fructose and mannose metabolism, tyrosine metabolism, etc. Additionally, oral administration of L. brevis FZU0713 significantly regulated the mRNA levels of liver genes (including Acat2, Acox1, Hmgcr, Cd36, Srebp-1c and Cyp7a1) involved in lipid metabolism and bile acid homeostasis. In conclusion, our findings provide the evidence that L. brevis FZU0713 has the potential to improve disturbance of lipid metabolism by regulating intestinal microflora and liver metabonomic profile. Therefore, L. brevis FZU0713 may be used as a potential probiotic strain to produce functional food to prevent hyperlipidemia.

Microbial community succession in soil is mainly driven by carbon and nitrogen contents rather than phosphorus and sulphur contents

Organic manure is widely applied in agricultural systems to improve soil nutrient cycling and other physicochemical properties. However, the biotic and abiotic mechanisms that drive C, N, P, and S cycling following manure application are not completely understood. In this study, soil samples were collected from long-term experimental plots that had been amended with farmyard manure or mineral fertilisers since 1964. Isotope labelling with 15N, 33P, and 35S; metagenomics; and high-throughput sequencing were used to reveal the relationships between C, N, P, and S dynamics and microbial community composition and functions depending on fertilisation. A clear niche differentiation was observed between bacteria and fungi under mineral and manure regimes. A network analysis showed that long-term manure application reduced the complexity and stability of soil microbial network. Furthermore, a variation partitioning analysis based on redundancy analysis indicated that microbial community variation was mainly driven by soil Cand N contents. Dissolved organic C was the most important factor regulating microbial community structure. Soil C and N contents explained 43.5% of bacterial and 37.9% of fungal community variations. In contrast, soil P and S contents explained 29.9% of bacterial and 20.3% of fungal community variations. Long-term manure application increased the abundance of most functional genes related to C, N, P, and S cycling. This led to increased C and N cycling rates under manure application, which provided sufficient substrates for microbial growth. Partial least squares path modelling indicated that soil physicochemical properties, especially dissolved organic carbon, directly influenced C and S cycling, whereas the N and P cycles were indirectly affected by the changes in microbial community composition. These results provide a new perspective on both direct and indirect effects of organic manure and inorganic fertilisers on the soil nutrient cycling processes mediated by soil microbial community.

Microbial dysbiosis precedes signs of sea star wasting disease in wild populations of Pycnopodia helianthoides

Sea star wasting (SSW) disease, a massive and ongoing epidemic with unknown cause(s), has led to the rapid death and decimation of sea star populations with cascading ecological consequences. Changes in microbial community structure have been previously associated with SSW, however, it remains unknown if SSW-associated dysbiosis is a mechanism or artifact of disease progression, particularly in wild populations. Here, we compare the microbiomes of the sunflower sea star, Pycnopodia helianthoides, before (Naïve) and during (Exposed and Wasting) the initial outbreak in Southeast Alaska to identify changes and interactions in the microbial communities associated with sea star health and disease exposure. We found an increase in microbial diversity (both alpha and beta diversity) preceding signs of disease and an increase in abundance of facultative and obligate anaerobes (most notably Vibrio) in both Exposed (apparently healthy) and Wasting animals. Complementing these changes in microbial composition was the initial gain of metabolic functions upon disease exposure, and loss of function with signs of wasting. Using Bayesian network clustering, we found evidence of dysbiosis in the form of co-colonization of taxa appearing in large numbers among Exposed and Wasting individuals, in addition to the loss of communities associated with Naïve sea stars. These changes in community structure suggest a shared set of colonizing microbes that may be important in the initial stages of SSW. Together, these results provide several complementary perspectives in support of an early dysbiotic event preceding visible signs of SSW.

Skin microbiome in atopic dermatitis: New insights from clinical trials.

Atopic dermatitis (AD) is a chronic skin inflammatory disorder, with extensive burden among both children and adults.1 Recent advances in mechanistic understanding of underlying inflammatory pathways associated with AD phenotypes have resulted in improved options for topical and systemic treatment,2 with efficacy of monotherapies (e.g. abrocitinib, baricitinib, dupilumab, lebrikizumab, nemolizumab, tralokinumab, upadacitinib) ranging from 56.7% to 83.6%.3 Progression of AD is influenced by a combination of genetic, environmental and microbial covariates, and several studies have demonstrated the potential role of skin resident microbial flora (especially the bacterium Staphylococcus aureus) in AD,4 which may also impact response to therapy. Pertinent to this topic, Rauer et al.5 present their results from microbiome analysis of skin samples collected from patients with AD in the current issue of The Journal of the European Academy of Dermatology and Venereology. The authors analyzed baseline demographic and microbiome data from 60 moderate-to-severe AD patients from a previously reported cohort in New York, USA, to investigate correlation between disease severity and composition of the skin microbiome. Skin microbiome was sampled by swabbing lesional and adjacent non-lesional skin, and characterized by sequencing hypervariable regions V1–V3 of the 16S rRNA gene. Severity of AD was determined using SCORAD (SCORing Atopic Dermatitis), the validated clinical tool used to assess the extent and severity of eczema. Rauer et al. used objective SCORAD (oSCORAD, which considers only extent and intensity of AD) to determine correlation of AD severity with microbiome. These authors reported the skin microbiome of AD patients was dominated by S. aureus, which was detected in 79% of samples and was the most abundant species in 49% of lesional and 28% of non-lesional samples. Interestingly, diversity of skin microbiome correlated with oSCORAD, with lower diversity in lesional skin compared to non-lesional skin. High AD severity was associated with low evenness (a key determinant of microbiome composition), independent of skin sampling location. These results indicate dysbiosis in the microbiome population in lesional skin. Moreover, these authors identified S. aureus as a major contributor to association of microbiome diversity with AD severity and AD-affected skin sites. Among clinical variables, ethnicity was found to be an important covariate in the association between AD severity and skin microbiome. However, given the small sample size for sub-group analysis in the study, the contribution of ethnicity to skin microbiome and AD severity warrants further investigation. While elevated levels of S. aureus in the skin microbiome of AD patients have previously been reported,4 the study by Rauer et al.5 underscores the clinical relevance of this association as the samples were collected from patients at baseline of a well-designed clinical trial. Further analysis of skin microbiome during the progression of disease is likely to shed important insight into the interplay between changes in microbial composition and response to therapy. Given these interesting findings, a reasonable next step could be inclusion of skin microbiome sampling into clinical trials as exploratory endpoints in future clinical trials of AD. This would allow assessment if the identified microbial changes are linked with patient outcomes or medication response in a controlled setting. Ultimately this may then allow patient stratification based on microbial composition. Expanding those findings beyond the microbiome, such as targeting skin fungal mycobiome or virome may also reveal new insights into the contribution of microbial populations in AD. An important clinical implication of these results is that abundance of S. aureus may be used as a surrogate for skin microbial dysbiosis, especially since this organism may be more easily measured in a clinical setting using quantitative PCR rather than complete or complex microbiome analysis. Sequencing results can subsequently be obtained to analyze the microbiome, and used as a validation tool. The current study by Rauer et al.5 highlights key relationships between the skin microbiome and severity of AD, and will greatly inform ongoing efforts to develop new personalized therapeutic options for this disease. The authors have no conflicts of interest to declare. Data sharing is not applicable to this article as no new data were created or analyzed in this study.

The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland.

The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no "decoupling" in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the "monopoly" of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.

The digestive fate of beef versus plant-based burgers from bolus to stool

Ultra-processed, plant-based burgers (PB) and traditional comminuted-beef burgers (BB) share similar organoleptic characteristics, yet a knowledge gap exists in understanding how consumption of these divergent physical structures alters the lipemic response and gut microbiota. PB, comprised of highly refined ingredients, is formulated with no intact whole food structure, while BB entraps lipids throughout the myofibrillar protein network. PB presented significantly higher free fatty acid (FFA) bioaccessibility (28.2 ± 4.80 %) compared to BB (8.73 ± 0.52 %), as obtained from their FFA release profiles over digestion time after characterizing them with a modified logistic model (SLM), using the simulated TIM Gastro-Intestinal Model (TIM-1). Additionally, the rate of lipolysis, k, obtained from the SLM for PB (90% CI [0.0175, 0.0277] min−1) was higher than for BB (90% CI [0.0113, 0.0171] min−1). Using the Simulated Human Intestinal Microbial Ecosystem (SHIME®), the Firmicutes to Bacteroidetes ratio (F/B ratio) was significantly higher for PB than BB; and linear discriminant analysis effect size (LEfSe) showed Clostridium and Citrobacter were more highly represented in the microbial community for the PB feed, whereas BB feed differentially enriched Megasphaera, Bacteroides, Alistipes, and Blautia at the genus level. Additionally, short-chain fatty acid (SCFA) production was altered (p < 0.05) site-specifically in each colon vessel, which could be attributed to the available substrates and changes in microbial composition. Total SCFAs were significantly higher for PB in the ascending colon (AC) and descending colon (DC) but higher for BB only in the transverse colon (TC). This research illustrates the crucial role of meat analog physical structure in modulating nutritional aspects beyond food composition alone.

Effects of Adding Lean Red Meat to a U.S.-Style Healthy Vegetarian Dietary Pattern on Gut Microbiota and Cardiovascular Risk Factors in Young Adults: a Crossover Randomized Controlled Trial

BackgroundLimited research evidence exists on the effects of red meat on gut microbiota in human adults. ObjectiveWe aim to assess the effects of consuming a Healthy U.S.-Style Dietary Pattern (HDP), without or with unprocessed or processed lean red meats, on gut microbiota and fecal short-chain fatty acid (SCFA) levels in healthy young adults. Secondary outcomes are cardiovascular disease risk factors. MethodsWe conducted a randomized, controlled, crossover trial with 3 3-wk dietary interventions, each separated by a 5-wk washout period with habitual dietary intake. Nineteen participants (8 females, age 26 ± 4 y old, BMI 23 ± 3 kg/m2) consumed 3 study diets in random order: 1) healthy lacto-ovo vegetarian diet (LOV); 2) LOV plus 3 ounces/d of cooked unprocessed lean red meat (URM); and 3) LOV plus 3 ounces/d of cooked processed lean red meat (PRM). Fecal and fasting blood samples were collected before and during the last 2 wk of each intervention. We measured fecal bacterial community structure using 16S rRNA amplicon sequencing (V4 region, primers 515F-806R). Community diversity, structure, and taxonomic composition were computed using Mothur v.1.44.3. ResultsThe addition of unprocessed or processed lean red meats to a LOV HDP did not influence short-term changes in bacterial taxonomic composition. Independent of red meat intake, the HDP led to changes in 23 bacteria; reductions in serum total cholesterol (TC) and LDL-C concentrations; but no changes in fecal SCFA, serum triglycerides, HDL-C concentrations, TC/HDL-C ratio, or blood pressures. With data from all 3 diet interventions combined, changes in some bacteria were associated with improvements in TC, LDL-C, triglycerides, and HDL-C concentrations, and TC/HDL-C ratio. ConclusionsHealthy young adults who adopt an HDP that may be vegetarian or omnivorous, including lean red meat, experience short-term changes in gut microbial composition, which associate with improvements in multiple lipid-related cardiovascular risk factors.NCT03885544, https://clinicaltrials.gov/ct2/show/NCT03885544?cond=NCT03885544&draw=2&rank=1

Effects of Variation in Tamarix chinensis Plantations on Soil Microbial Community Composition in the Middle Yellow River Floodplain

Floodplains have important ecological and hydrological functions in terrestrial ecosystems, experience severe soil erosion, and are vulnerable to losing soil fertility. Tamarix chinensis Lour. plantation is the main vegetation restoration measure for maintaining soil quality in floodplains. Soil microorganisms are essential for driving biogeochemical cycling processes. However, the effects of sampling location and shrub patch size on soil microbial community composition remain unclear. In this study, we characterized changes in microbial structure, as well as the factors driving them, in inside- and outside-canopy soils of three patch sizes (small, medium, large) of T. chinensis plants in the middle Yellow River floodplain. Compared with the outside-canopy soils, inside-canopy had higher microbial phospholipid fatty acids (PLFAs), including fungi, bacteria, Gram-positive bacteria (GP), Gram-negative bacteria (GN), and arbuscular mycorrhizal fungi. The ratio of fungi to bacteria and GP to GN gradually decreased as shrub patch size increased. Differences between inside-canopy and outside-canopy soils in soil nutrients (organic matter, total nitrogen, and available phosphorus) and soil salt content increased by 59.73%, 40.75%, 34.41%, and 110.08% from small to large shrub patch size. Changes in microbial community composition were mainly driven by variation in soil organic matter, which accounted for 61.90% of the variation in inside-canopy soils. Resource islands could alter microbial community structure, and this effect was stronger when shrub patch size was large. The results indicated that T. chinensis plantations enhanced the soil nutrient contents (organic matter, total nitrogen, and available phosphorus) and elevated soil microbial biomass and changed microbial community composition; T. chinensis plantations might thus provide a suitable approach for restoring degraded floodplain ecosystems.

Effects of salinity on growth, physiology, biochemistry and gut microbiota of juvenile grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is among the most important freshwater fish species in China. However, it remained unclear how salinity could affect grass carp. Two experiments were performed. The first experiment was a 4-day acute salt tolerance experiment with six salinities (0, 4, 8, 12, 16, and 20 ppt). The second experiment was an 8-week chronic salt stress experiment with three salinities (0, 2 and 6 ppt). To investigate the intestinal bacterial community of grass carp from three salinities (0, 2, and 6 ppt), the 16S rDNA sequencing was performed. The results showed that grass carp exhibited great adaptability to low salinity (2 ppt), with no significant difference in growth and maintained stable physiological and immune status. However, exposed to high salinity (6 ppt) caused significant deleterious effects on grass carp, including growth inhibition as well as physiological and immune-related changes. The gut microbiota in grass carp changed with salinity. With the increase of salinity, the proportion of beneficial bacteria in the gut of grass carp gradually decreased, while some harmful bacteria gradually occupied the dominant position. Changes in gut microbial composition ultimately affected the growth of grass carp. This study helps further clarify the effects of salinity on grass carp.

Endogenous small intestinal microbiome determinants of transient colonisation efficiency by bacteria from fermented dairy products: a randomised controlled trial

BackgroundThe effects of fermented food consumption on the small intestine microbiome and its role on host homeostasis are largely uncharacterised as our knowledge on intestinal microbiota relies mainly on faecal samples analysis. We investigated changes in small intestinal microbial composition and functionality, short chain fatty acid (SCFA) profiles, and on gastro-intestinal (GI) permeability in ileostomy subjects upon the consumption of fermented milk products.ResultsWe report the results from a randomised, cross-over, explorative study where 16 ileostomy subjects underwent 3, 2-week intervention periods. In each period, they consumed either milk fermented by Lacticaseibacillus rhamnosus CNCM I-3690, or milk fermented by Streptococcus thermophilus CNCM I-1630 and Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, or a chemically acidified milk (placebo) daily. We performed metataxonomic, metatranscriptomic analysis, and SCFA profiling of ileostomy effluents as well as a sugar permeability test to investigate the microbiome impact of these interventions and their potential effect on mucosal barrier function. Consumption of the intervention products impacted the overall small intestinal microbiome composition and functionality, mainly due to the introduction of the product-derived bacteria that reach in several samples 50% of the total microbial community. The interventions did not affect the SCFA levels in ileostoma effluent, or gastro-intestinal permeability and the effects on the endogenous microbial community were negligible. The impact on microbiome composition was highly personalised, and we identified the poorly characterised bacterial family, Peptostreptococcaceae, to be positively associated with a low abundance of the ingested bacteria. Activity profiling of the microbiota revealed that carbon- versus amino acid-derived energy metabolism of the endogenous microbiome could be responsible for the individual-specific intervention effects on the small intestine microbiome composition and function, reflected also on urine microbial metabolites generated through proteolytic fermentation.ConclusionsThe ingested bacteria are the main drivers of the intervention effect on the small intestinal microbiota composition. Their transient abundance level is highly personalised and influenced by the energy metabolism of the ecosystem that is reflected by its microbial composition (http://www.clinicaltrials.gov, ID NCT NCT02920294).3z8GaJs8-4AmNdyX8busiEVideo

Metatranscriptomic insights into the microbial electrosynthesis of acetate by Fe2+/Ni2+ addition.

As important components of enzymes and coenzymes involved in energy transfer and Wood-Ljungdahl (WL) pathways, Fe2+ and Ni2+ supplementation may promote the acetate synthesis through CO2 reduction by the microbial electrosynthesis (MES). However, the effect of Fe2+ and Ni2+ addition on acetate production in MES and corresponding microbial mechanisms have not been fully studied. Therefore, this study investigated the effect of Fe2+ and Ni2+ addition on acetate production in MES, and explored the underlying microbial mechanism from the metatranscriptomic perspective. Both Fe2+ and Ni2+ addition enhanced acetate production of the MES, which was 76.9% and 110.9% higher than that of control, respectively. Little effect on phylum level and small changes in genus-level microbial composition was caused by Fe2+ and Ni2+ addition. Gene expression of 'Energy metabolism', especially in 'Carbon fixation pathways in prokaryotes' was up-regulated by Fe2+ and Ni2+ addition. Hydrogenase was found as an important energy transfer mediator for CO2 reduction and acetate synthesis. Fe2+ addition and Ni2+ addition respectively enhanced the expression of methyl branch and carboxyl branch of the WL pathway, and thus promoted acetate production. The study provided a metatranscriptomic insight into the effect of Fe2+ and Ni2+ on acetate production by CO2 reduction in MES.

Dynamic changes of microbial community composition and diversity in metal contaminated and reclaimed lands assessed by Illumina MiSeq sequencing

Dynamic changes of microbial community composition and diversity in metal contaminated and reclaimed lands assessed by Illumina MiSeq sequencing

Effects of ileocolonic delivered vitamin B2, B3 and C (ColoVit) or the Groningen anti-inflammatory diet on disease course and microbiome of patients with Crohn’s disease (VITA-GrAID study): a protocol for a randomised and partially blinded trial

BackgroundDiet plays a pivotal role in the onset and progression of Crohn’s disease (CD). Nutritional interventions revealed effects on intestinal inflammation and gut microbial composition. However, data from well-designed and...

Soil Microbial Biomass and Community Composition across a Chronosequence of Chinese Cedar Plantations

Afforestation is one of the most important forestry practices, but its impact on soil microbial communities remains poorly understood. In this study, we sampled the soil from 0–15 cm and 15–30 cm soil depths of 7-, 13-, 24-, 33-, and 53-year-old Chinese cedar (Cryptomeria japonica var. sinensis) plantations. To investigate the effect of stand age on soil microbial communities and their potential drivers, we measured phospholipid fatty acids (PLFAs) and soil physicochemical properties. At the 0–15 cm soil depth, the biomass of total PLFAs and functional microbial groups such as bacteria (B), fungi (F), Gram-negative bacteria (GN), Gram-positive bacteria (GP), actinomycetes (ACT), and arbuscular mycorrhizal fungi (AMF) increased sharply in 7- to 13-year-old stands, but then gradually leveled off in older stands. On the other hand, the biomass of total PLFAs and functional microbial groups at the 15–30 cm soil depth peaked in the 33-year-old stand. The biomass of total PLFAs and functional microbial groups was strongly influenced by stand age and soil depth, and was significantly lower at the 15–30 cm soil depth than at the 0–15 cm soil depth except for the 7-year-old stand. The F/B and fungi/total PLFAs ratios of both soil depths were markedly lower in the 13-year-old stand than in the remaining four stand ages, while the proportions of the bacterial group (GP and GN) showed contrasting trends. The biomass of all functional microbial groups and the GP/GN ratio were mainly mediated by soil organic carbon (SOC) concentration and the soil organic carbon to total phosphorus (C/P) ratio at the 0–15 cm soil depth, but primarily affected by ammonium nitrogen (NH4+-N) concentration at the 15–30 cm soil depth. The F/B ratio of the two soil depths was prominently affected by nitrate nitrogen (NO3−-N) concentration. Our results highlighted that SOC concentration and mineral N (i.e., NH4+-N and NO3−-N) concentration mainly drove changes in the soil microbial biomass and community composition with stand age in Chinese cedar plantations, and that the 13-year-old stand may be the key period for management.

Oligosaccharides isolated from Rehmannia glutinosa protect LPS-induced intestinal inflammation and barrier injury in mice.

We investigated the protective effect of Rehmannia glutinosa oligosaccharides (RGO) on lipopolysaccharide (LPS)-induced intestinal inflammation and barrier injury among mice. RGO is prepared from fresh rehmannia glutinosa by water extraction, active carbon decolorization, ion exchange resin impurity removal, macroporous adsorption resin purification, and decompression drying. LPS could establish the model for intestinal inflammation and barrier injury in mice. Three different doses of RGO were administered for three consecutive weeks. Then the weight, feces, and health status of the mice were recorded. After sacrificing the mice, their colon length and immune organ index were determined. The morphological changes of the ileum and colon were observed using Hematoxylin-eosin (H&E) staining, followed by measuring the villus length and recess depth. RT-qPCR was utilized to detect the relative mRNA expression of intestinal zonula occludens-1 (ZO-1) and occludin. The expression of inflammatory factors and oxidation markers within ileum and colon tissues and the digestive enzyme activities in the ileum contents were detected using ELISA. The content of short-chain fatty acids (SCFAs) in the colon was determined with GC. The gut microbial composition and diversity changes were determined with 16S-rRNA high-throughput sequencing. The association between intestinal microorganisms and SCFAs, occludins, digestive enzymes, inflammatory factor contents, and antioxidant indexes was also analyzed. RGO significantly increased the weight, pancreatic index, thymus index, and colon length of mice compared with the model group. Moreover, it also improved the intestinal tissue structure and increased the expression of intestinal barrier-related junction proteins ZO-1 and Occludin. The contents of IL-6, IL-17, IL-1β, and TNF-α in the intestinal tissues of mice were significantly reduced. Additionally, the activities of superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and catalase (CAT) were elevated. In contrast, the malondialdehyde (MDA) content decreased. Trypsin and pancreatic lipase activities in the ileum enhanced, and the SCFA contents such as acetic acid, propionic acid, and butyric acid in the colon increased. The study on intestinal flora revealed that RGO could enhance the abundance of intestinal flora and improve the flora structure. After RGO intervention, the relative abundance of Firmicutes, Lactobacillus, and Akkermania bacteria in the intestinal tract of mice increased compared with the model group, while that of Actinomycetes decreased. The intestinal microbiota structure changed to the case, with probiotics playing a dominant role. The correlation analysis indicated that Lactobacillus and Ackermann bacteria in the intestinal tract of mice were positively associated with SCFAs, Occludin, ZO-1, pancreatic amylase, SOD, and CAT activities. Moreover, they were negatively correlated with inflammatory factors IL-6, IL-17, IL-1β, and TNF-α. RGO can decrease LPS-induced intestinal inflammation and intestinal barrier injury in mice and protect their intestinal function. RGO can ameliorate intestinal inflammation and maintain the intestinal barrier by regulating intestinal flora.

Adaptation of Rhizosphere Microbial Communities to Continuous Exposure to Multiple Residual Antibiotics in Vegetable Farms.

The constant application of manure-based fertilizers in vegetable farms leads to antibiotic residue accumulation in soils, which has become a major stressor affecting agroecosystem stability. The present study investigated the adaptation profiles of rhizosphere microbial communities in different vegetable farms to multiple residual antibiotics. Multiple antibiotics, including trimethoprim, sulfonamides, quinolones, tetracyclines, macrolides, lincomycins, and chloramphenicols, were detected in the vegetable farms; the dominant antibiotic (trimethoprim) had a maximum concentration of 36.7 ng/g. Quinolones and tetracyclines were the most prevalent antibiotics in the vegetable farms. The five most abundant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Firmicutes, while the five most abundant phyla in root samples were Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Myxococcota. Macrolides were significantly correlated with microbial community composition changes in soil samples, while sulfonamides were significantly correlated with microbial community composition changes in root samples. Soil properties (total carbon and nitrogen contents and pH) influenced the shifts in microbial communities in rhizosphere soils and roots. This study provides evidence that low residual antibiotic levels in vegetable farms can shift microbial community structures, potentially affecting agroecosystem stability. However, the degree to which the shift occurs could be regulated by environmental factors, such as soil nutrient conditions.

Microbial community succession patterns and drivers of Luxiang-flavor Jiupei during long fermentation.

Luxiang-flavor Baijiu is the mainstream of Baijiu production and consumption in China, and the microbial composition has a great influence on the flavor and quality of Baijiu. In this study, we combined multi-omics sequencing technology to explore the microbial composition, dynamics and metabolite changes of Luxiang-flavor Jiupei during long fermentation periods. The results showed that based on the interaction between environmental constraints and microorganisms, Jiupei microorganisms formed different ecological niches and functional differentiation, which led to the formation of Jiupei stable core microorganisms. The bacteria were mainly Lactobacillus and Acetobacter, and the fungi were mainly Kazachstani and Issatchenkia. Most bacteria were negatively correlated with temperature, alcohol and acidity, and for the fungi, starch content, reducing sugar content and temperature had the most significant effects on community succession. Macroproteomic analysis revealed that Lactobacillus jinshani had the highest relative content; microbial composition, growth changes and functions were more similar in the pre-fermentation period (0-18 days); microorganisms stabilized in the late fermentation period (24-220 days). The metabolome analysis revealed that the metabolites of the Jiupei changed rapidly from 18 to 32 days of fermentation, with a significant increase in the relative content of amino acids, peptides and analogs and a significant decrease in the relative content of sugars; the metabolites of the Jiupei changed slowly from 32 to 220 days of fermentation, with a stabilization of the content of amino acids, peptides and analogs. This work provides insights into the microbial succession and microbial drivers during the long-term fermentation of Jiupei, which have potential implications for optimizing production and improving the flavor of Baijiu.

No evidence that modification of soil microbiota by woody invader facilitates subsequent invasion by herbaceous species.

Many terrestrial ecosystems are co-invaded by multiple exotic species. The "invasional meltdown" hypothesis predicts that an initial invasive species will facilitate secondary invasions. In the plant kingdom, the potential underlying mechanisms of this hypothesis may be that modification of the soil properties by the initial invaders benefits for the subsequent exotic species invasion. In this study, we analyzed the composition of soil microbial communities and soil chemical properties from sites invaded by woody Rhus typhina, as well as uninvaded sites, to assess the impact of R. typhina invasion. Furthermore, we conducted a greenhouse experiment with multiple native-invasive pairs of herbaceous species to test whether R. typhina invasion facilitates subsequent exotic herb invasion. Our results showed that R. typhina invasion significantly altered the composition of soil fungal communities, especially pathogenic, endophytic, and arbuscular mycorrhizal fungi. However, this change in microbial composition led to neither direction nor magnitude changes in negative plant-soil feedback effects on both native and invasive species. This indicates that initial R. typhina invasion does not facilitate subsequent herb invasion, which does not support the "invasional meltdown" hypothesis. Additionally, R. typhina invasion significantly decreased soil total nitrogen and organic carbon contents, which may explain the significantly lower biomass of herbaceous roots grown in invaded soils compared with uninvaded soils. Alternately, although invasive herb growth was significantly more inhibited by soil microbiota compared with native herb growth, such inhibition cannot completely eliminate the risk of exotic herb invasion because of their innate growth advantages. Therefore, microbial biocontrol agents for plant invasion management should be combined with another approach to suppress the innate growth advantages of exotic species.