High-throughput 16S rRNA Gene Sequencing Research Articles

Avian leukosis virus subgroup J infection influences the gut microbiota composition in Huiyang bearded chickens.

Avian leukosis virus (ALV) poses a major threat to poultry. The chicken gut microbiota plays critical roles in host performance, health and immunity. However, the effect of viral infection on the microbiota of Chinese local chickens is not well understood. In this study, we performed high-throughput 16S rRNA gene sequencing and evaluated the gut microbiota profiles using faeces from ALV subgroup J (ALV-J)-infected and healthy Huiyang bearded chickens (Chinese local chickens). At the phylum level, ALV-J infection mainly increased the abundance of Bacteroidetes and Proteobacteria and decreased that of Firmicutes. An analysis at the order, family and genus levels showed that the abundance of Lactobacillales, Lactobacillaceae and Lactobacillus was the highest in normal chicken faeces, accounting for 89·07%, 86·47% and 86·46%, respectively, of phylotypes. Moreover, samples from ALV-J-infected chickens were enriched with Bacteroidales, Clostridiales, Bacteroidaceae, Ruminococcaceae, Lachnospiraceae and Bacteroides. Our findings highlight that ALV-J infection alters the gut microbiota and disrupts the host-microbial homeostasis in chickens, which may be involved in the pathogenesis of ALV-J infection.

Polar Cryoconite Associated Microbiota Is Dominated by Hemispheric Specialist Genera.

Cryoconite holes, supraglacial depressions containing water and microbe-mineral aggregates, are known to be hotspots of microbial diversity on glacial surfaces. Cryoconite holes form in a variety of locations and conditions, which impacts both their structure and the community that inhabits them. Using high-throughput 16S and 18S rRNA gene sequencing, we have investigated the communities of a wide range of cryoconite holes from 15 locations across the Arctic and Antarctic. Around 24 bacterial and 11 eukaryotic first-rank phyla were observed in total. The various biotic niches (grazer, predator, photoautotroph, and chemotroph), are filled in every location. Significantly, there is a clear divide between the bacterial and microalgal communities of the Arctic and that of the Antarctic. We were able to determine the groups contributing to this difference and the family and genus level. Both polar regions contain a “core group” of bacteria that are present in the majority of cryoconite holes and each contribute >1% of total amplicon sequence variant (ASV) abundance. Whilst both groups contain Microbacteriaceae, the remaining members are specific to the core group of each polar region. Additionally, the microalgal communities of Arctic cryoconite holes are dominated by Chlamydomonas whereas the Antarctic cryoconite holes are dominated by Pleurastrum. Therefore cryoconite holes may be a global feature of glacier landscapes, but they are inhabited by regionally distinct microbial communities. Our results are consistent with the notion that cryoconite microbiomes are adapted to differing conditions within the cryosphere.

Bacterioneuston and Bacterioplankton Structure and Abundance in Two Trophically Distinct Marine Environments - a Marine Lake and the Adjacent Coastal Site on the Adriatic Sea.

Marine surface microlayer (SML) is a large and extreme marine environment with an important role in biogeochemical cycling and climate regulation. We explored the seasonal structure and abundance of bacterial assemblages in SML (bacterioneuston) and underlying water layer (ULW) (bacterioplankton) in eutrophic marine Rogoznica Lake and more oligotrophic coastal area of the adjacent Adriatic Sea. SML and ULW in each site were similar in pH, salinity, dissolved oxygen, oxygen saturation, and temperature. Rogoznica Lake was colder in winter and warmer in summer compared to the Adriatic Sea. Regarding nutrients, SML and ULW were notably different environments. SML was consistently enriched in nitrate, nitrite, orthophosphate, and total organic carbon than ULW in both investigated environments. Except in spring in Rogoznica Lake, bacterial abundance in SML was also significantly higher (p < 0.05) than in ULW. Both layers and sites show prominent seasonal variability. High-throughput 16S rRNA gene sequencing of DNA and cDNA revealed a considerable difference in bacterial assemblage structure, although study sites were < 200m apart. Heterotrophs were predominant in both layers with pronounced spatial and temporal structural differences, except in autumn in Rogoznica Lake when, autotrophs became the dominant fraction under oxygen-deprived conditions. All these variations were driven by in situ conditions, the most important ones being total organic carbon and temperature (and additionally dissolved oxygen in Rogoznica Lake). This is especially important in terms of ongoing eutrophication, warming and deoxygenation, noticed not only in the Adriatic Sea and Rogoznica Lake but globally as well. Therefore, further structural and physiological changes in bacterioneuston and bacterioplankton assemblages can be expected.

The Clinical Utility of Two High-Throughput 16S rRNA Gene Sequencing Workflows for Taxonomic Assignment of Unidentifiable Bacterial Pathogens in Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.

ABSTRACTBacterial pathogens that cannot be identified using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) are occasionally encountered in clinical laboratories. The 16S rRNA gene is often used for sequence-based analysis to identify these bacterial species. Nevertheless, traditional Sanger sequencing is laborious, time-consuming, and low throughput. Here, we compared two commercially available 16S rRNA gene sequencing tests that are based on Illumina and Nanopore sequencing technologies, respectively, in their ability to identify the species of 172 clinical isolates that failed to be identified by MALDI-TOF MS. Sequencing data were analyzed by the respective built-in programs (MiSeq Reporter software of Illumina and Epi2me of Nanopore) and BLAST+ (v2.11.0). Their agreement with Sanger sequencing on species-level identification was determined. Discrepancies were resolved by whole-genome sequencing. The diagnostic accuracy of each workflow was determined using the composite sequencing result as the reference standard. Despite the high base-calling accuracy of Illumina sequencing, we demonstrated that the Nanopore workflow had a higher taxonomic resolution at the species level. Using built-in analysis algorithms, the concordance of Sanger 16S with the Illumina and Nanopore workflows was 33.14% and 87.79%, respectively. The agreement was 65.70% and 83.14%, respectively, when BLAST+ was used for analysis. Compared with the reference standard, the diagnostic accuracy of Nanopore 16S was 96.36%, which was identical to that of Sanger 16S and better than that of Illumina 16S (69.07%). The turnaround time of the Illumina workflow and the Nanopore workflow was 78 h and 8.25 h, respectively. The per-sample cost of the Illumina and Nanopore workflows was US$28.5 and US$17.7, respectively.

Autochthonous fungi are central components in microbial community structure in raw fermented sausages.

SummaryRaw meat sausage represents a unique ecological niche rich in nutrients for microbial consumption, making it particularly vulnerable to microbial spoilage. Starter cultures are applied to improve product stability and safety as well as flavour characteristics. However, the influence of starter cultures on microbial community assembly and succession throughout the fermentation process is largely unknown. In particular the effect on the fungal community has not yet been explored. We evaluate the microbiological status of four different raw meat sausages using high‐throughput 16S rRNA gene and ITS2 gene sequencing. The objective was to study temporal changes of microbial composition during the fermentation process and to identify potential keystone species that play an important role within the microbial community. Our results suggest that fungi assigned to the species Debaryomyces hansenii and Alternaria alternata play a key role in microbial community dynamics during fermentation. In addition, bacteria related to the starter culture Lactobacillus sakei and the spoilage‐associated genera Acinetobacter, Pseudomonas and Psychrobacter are central components of the microbial ecosystem in raw fermented sausages. Elucidating the exact role and interactions of these microorganisms has the potential to have direct impacts on the quality and safety of fermented foods.

Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River

Suspended particles in water can shelter both microorganisms and contaminants. However, the emerging pollutants antibiotic resistance genes (ARGs) in free-living (FL) or particle-attached (PA) bacteria in aquatic environments are less explored. In this study, we compared the free-living and particle-attached ARGs during four seasons in the Yellow River using high-throughput quantitative PCR techniques and 16S rRNA gene sequencing. Our results demonstrated that both the free-living water and particles were dominated by tetracycline and beta-lactamase resistance genes. The PA-ARGs had a higher absolute abundance than FL-ARGs in the Yellow River, regardless of the season. Both PA-ARGs and FL-ARGs had the highest absolute abundance and diversity during winter. Mobile genetic elements (MGEs) were the dominant driver for both size-fractionated ARGs. However, the microbiome had less influence on PA-ARG profiles than the FL-ARG profiles, while the effects of the heavy metals on ARGs were negligible. The community assembly of both FL-ARG and PA-ARG can be explained by neutral processes. Several opportunistic pathogens (e.g., Escherichia coli) associated with human health exhibited a higher relative abundance in the particles than during a free-living lifestyle. Parts of these pathogens were potential ARG hosts. As such, it is important to monitor the ARGs and opportunistic pathogens from size-fractionated bacteria and develop targeted strategies to manage ARG dissemination and opportunistic pathogens to ensure public health.

Carbon sources driven supernatant micro-particles differentiate in submerged anaerobic membrane bioreactors (AnMBRs)

Recently, micro-particles with a size range of 0.45–10 μm in anaerobic membrane bioreactors (AnMBRs), were rich in microorganisms and characterized as a significant source to membrane fouling. Nevertheless, little is known about the formation of the micro-particles associated microorganisms as well as their metabolic functions, which could be largely impacted by carbon sources in the influent. Here, protein and glucose were chosen to be two different carbon sources fed into two identical AnMBRs (i.e., AnMBR-P and AnMBR-G), and a comprehensive comparison of the micro-particles formed in corresponding reactors was made. Size-dependent fractionation and fluorescent staining assay showed that micro-particles with the size range of 0.45–1 μm possessed the highest contents (41.4%) in the AnMBR-P and presented as vibrios and coccus, while the 5–10 μm micro-particles with filamentous morphologies were the prevailing fraction (61.9%) in the AnMBR-G. According to the results of high-throughput 16S rRNA gene sequencing, the Lentimicrobiaceae, D8A-2 and Syntrophorhabdus prevailed in the AnMBR-P micro-particles, while the SJA-15 showed overwhelming predominance than the other genera in the AnMBR-G micro-particles. Metagenomic sequencing further revealed that the micro-particles in the AnMBR-P possessed higher abundance in specific functional genes for nitrogen metabolism (nirB), sulfur metabolism (cysK) and cysteine and methionine metabolism (mtaD), as well as in the cell mobility as chemotaxis (rbsB) and flagellar assembly (fliC). In comparison, the micro-particles obtained from the AnMBR-G encoded abundant genes for converting glucose to metabolites in the next level, such as glk (glucokinase), pfk (ATP-dependent phosphofructokinase), and PGK (phosphoglycerate kinase). Overall, our findings provided new insights into the formation of micro-particles in the supernatant of AnMBRs, which could facilitate to propose related fouling alleviation methods from the perspective of carbon sources regulation and/or pretreatment of the influent.

The gut microbiome and metabolome of Himalayan Griffons (Gyps himalayensis): insights into the adaptation to carrion-feeding habits in avian scavengers

BackgroundHimalayan Griffons (Gyps himalayensis), large scavenging raptors widely distributed in Qinghai-Tibetan Plateau, have evolved a remarkable ability to feed on carcasses without suffering any adverse effects. The gut microbiome plays an important role in animal physiological and pathological processes, and has also been found to play a health protective role in the vulture adaptation to scavenging. However, the microbial taxonomic diversity (including nonculturable and culturable microbes), functions, and metabolites related to Himalayan Griffons have not been fully explored.MethodsIn the present study, the 28 fecal samples of the Himalayan Griffons and 8 carrion samples were collected and sequenced using high-throughput 16S rRNA gene sequencing methods to analyze the composition and functional structures of the microbiomes. Twelve fecal samples of the Himalayan Griffons were analyzed using untargeted Liquid Chromatography Mass Spectroscopy (LC–MS) to identify metabolites. We used different culture conditions to grow Himalayan Griffons gut microbes. Inhibitory effects of gut beneficial bacteria on 5 common pathogenic bacteria were also tested using the Oxford cup method.ResultsAccording to the results of the culture-independent method, a high abundance of four major phyla in Himalayan Griffons were identified, including Fusobacteria, Firmicutes, Bacteroidetes, and Proteobacteria. The most abundant genera were Fusobacterium, followed by Clostridium_sensu_stricto_1, Cetobacterium, Epulopiscium, and Bacteroides. The predicted primary functional categories of the Himalayan Griffons’ gut microbiome were associated with carbohydrate and amino acid metabolism, replication and repair, and membrane transport. LC–MS metabolomic analysis showed a total of 154 metabolites in all the fecal samples. Cultivation yielded 184 bacterial isolates with Escherichia coli, Enterococcus faecium, Enterococcus hirae, and Paeniclostridium sordellii as most common isolates. Moreover, 7 potential beneficial gut bacteria isolated showed certain inhibition to 5 common pathogenic bacteria.ConclusionsOur findings broaden and deepen the understanding of Himalayan Griffons’ gut microbiome, and highlighted the importance of gut microbiome-mediated adaptation to scavenging habits. In particular, our results highlighted the protective role of gut beneficial bacteria in the Himalayan Griffons against pathogenic bacteria that appear in rotten food resources.

Fluoride exposure cause colon microbiota dysbiosis by destroyed microenvironment and disturbed antimicrobial peptides expression in colon

Colon microenvironment and microbiota dysbiosis are closely related to various human metabolic diseases. In this study, a total of 72 healthy female mice were exposed to fluoride (F) (0, 25, 50 and 100 mg/L F−) in drinking water for 70 days. The effect of F on intestinal barrier and the diversity and composition in colon microbiota have been evaluated. Meanwhile, the relationship among F-induced colon microbiota alterations and antimicrobial peptides (AMPs) expression and short-chain fatty acids (SCFAs) level also been assessed. The results suggested that F decreased the goblet cells number and glycoprotein expression in colon. And further high-throughput 16S rRNA gene sequencing result demonstrated that F exposure induced the diversity and community composition of colonic microbiota significantly changes. Linear Discriminant Analysis Effect Size (LEfSe) analysis identified 11 predominantly characteristic taxa which may be the biomarker in response to F exposure. F-induced intestinal microbiota perturbations lead to the significantly decreased SCFAs levels in colon. Immunofluorescence results showed that F increased the protein expression of interleukin-17A (IL-17A) and IL-22 (P < 0.01) and disturbed the expression of interleukin-17 receptor A (IL-17RA) and IL-22R (P < 0.05 or P < 0.01). In addition, the increased expression of IL-17A and IL-22 cooperatively enhanced the mRNA expression of AMPs which response to F-induced microbiota perturbations. Collectively, destroyed microenvironment and disturbed AMPs are the primary reason of microbiota dysbiosis in colon after F exposure. Colonic homoeostasis imbalance would be helpful for finding the source of F-induced chronic systemic diseases.

PSVI-13 Changes in the taxonomic composition of the rumen of ruminants when introducing fat components into the diet

Abstract Fats are concentrated energy sources for cattle growth, but their inclusion in the diet has a huge impact on the taxonomic composition of the rumen. The aim of this study was to evaluate the effect of supplemental linseed oil administration (3% of dry matter (DM) diet) on microbiota and DM digestibility in the rumen. The studies carried out on Kazakh white-headed bull calves, aged 15 months, with chronic rumen fistula (diet - 70% grassland hay, 30% barley grain). Dietary dry matter digestibility (in-vitro in an artificial rumen system, for 24 hours) analyzed daily for 10 days, and microflora (fluid-bound) analyzed using high-throughput 16SrRNA gene sequencing (Illumina). Inclusion of LO showed a slight 3.5% increase in DM digestibility compared to C (52.0% versus 53.9%). The taxonomic composition of the rumen microbiocenosis in group C was mainly represented by the phylum Firmicutes (54.7%) and Bacteroidetes (39.3%), while other phylum numbers were less than 2%. When LO was injected, the dominance of phylum Bacteroidetes (64.2%), phylum Firmicutes (19.3%), and Verrucomicrobia (5.3%) was noted. The calculation of the Shannon index showed an increase in species diversity in the group that received LO. It was H’= 0.76, while in CH’= 0.42. The Simpson dominance index in group C was 0.44, in the group receiving LOD = 0.54. The obtained data show a positive effect. The linseed oil allow to increase the biodiversity of the rumen microbiome and the digestibility of DM feed, which can be used in fattening young cattle. This research performed with financial support from the project 0761-2019-0005.

Bioaugmentation with syntrophic volatile fatty acids-oxidizing consortia to alleviate the ammonia inhibition in continuously anaerobic digestion of municipal sludge

Ammonia inhibition easily affects the performance of anaerobic digestion (AD) for municipal sludge and the oxidization of volatile fatty acids (VFAs) is the rate-limiting step of this process. Bioaugmentation is considered to be an effective method to alleviate ammonia inhibition of AD, but most study used the hydrogenotrophic methanogens as the bioaugmentation culture. In this study, bioaugmentation of mesophilic AD (MAD) and thermophilic AD (TAD) under ammonia inhibition with syntrophic acetate and propionate oxidizing consortia was investigated. The results showed that the bioaugmented reactors recovered earlier than control reactors with 20 (MAD) and 8 (TAD) days, respectively. The high-throughput 16S rRNA gene sequencing indicated that the relative abundance of carbohydrates fermenter (Lentimicrobium), syntrophic VFAs-oxidizing bacteria (Rikenellaceae_DMER64, Smithella and Syntrophobacter) and acetoclastic and hydrogenotrophic methanogens (Methanosaeta, Methanolinea and Methanospirillum) increased in MAD after bioaugmentation. However, part of the bioaugmentation culture could not adapt to the high free ammonia (FAN) concentration in MAD and the effect was weakened. In TAD, proteolytic bacteria (Keratinibaculum and Tepidimicrobium), syntrophic VFAs-oxidizing bacteria (Syntrophomonas) and hydrogenotrophic methanogen (Methanosarcina) were strengthened. The effect of bioaugmentation in TAD was durable even at higher organic loading rate (OLR), due to its positive influence on microbial community. These results suggested that the different bioaugmentation mechanism occurred in MAD and TAD, which are derived from the synergetic effects of ammonia tolerance and microbial interactions. Our study revealed the VFAs-oxidizing consortia as bioaugmented culture could be the potential strategy to alleviate the ammonia stress of AD.

Dynamic changes in the intestinal microbial community of two time-aged soils under combined cadmium and ciprofloxacin contaminated conditions

The effects of combined contaminated soils containing cadmium (Cd) and ciprofloxacin (CIP) on the human gut microbiota are demonstrated using an in vitro test. Uncontaminated soil samples were artificially polluted with Cd and CIP using three different treatments (CK: 0 mg·kg−1; CIPI: 5 mg·kg−1, CIPII: 25 mg·kg−1, and Cd: 80 mg·kg−1). An experiment was performed to investigate the effect of Cd and CIP on the human colon microbiota using two aging times (D30: Day 30; D60: Day 60), and then the method of high-throughput 16S rRNA gene sequencing was used. In this study, we observed five phyla: Proteobacteria, Firmicutes, Synergistetes, Bacteroidetes, and Actinobacteria in colon microbial community. In addition, our results indicated that the relative abundances of the gut bacteria varied at the phylum level. Nevertheless, a slight decline in the relative abundance of Bacteroidetes among all the sets (compared to the D30-CK + Cd set) was revealed, and the lowest decline percentage of 90% was observed in the D60-CIPI + Cd set. Our results validated that the relative abundance of Rhodococcus increased with an increase in the CIP concentration in D30. In addition, this may disrupt normal physiological functions of the intestine after exposure to contaminated soil via the mouth. This study provides a theoretical basis for human risk assessment of oral exposure to Cd and CIP contaminated soils.

The effect of benzo[a]pyrene on the gut microbiota of Nile tilapia (Oreochromis niloticus).

Benzo[a]pyrene (BaP) is a highly toxic and carcinogenic polycyclic aromatic hydrocarbon (PAH) whose toxicological effects in the gut microbiota of aquatic organisms have not yet been fully revealed. Therefore, in this study, we used high-throughput 16S rRNA gene sequencing to evaluate the effects of BaP in the gut microbiome of Oreochromis niloticus, including its possible participation in the process of detoxification and its ability to recover. The fish were injected with a single intraperitoneal dose of 20mgkg-1 of BaP, and the effects in the microbiome were evaluated at 24, 72, and 120h post-injection. The results indicate a clear dysbiosis (in composition, relative abundance, diversity, and interaction networks) of the gut microbiota during 24h post-injection, dominated by Fusobacteria and Bacteroidetes and a decrease in Proteobacteria and Spirochaetae. Interestingly, a slight recovery of the microbiome begins at 72h and stabilises at 120h post-injection. Pathway analysis revealed the participation of the gut microbiome in PAH degradation mainly at 24h post-injection. This study provides new insights in the toxicology of BaP in O. niloticus and the first evidence of the ability of the gut microbiome to recovery after a chemical disturbance. KEY POINTS: • Benzo[a]pyrene caused a dysbiosis in the gut microbiota of Oreochromis niloticus. • We observed an enrichment of bacteria involved in the metabolism of xenobiotics. • The gut microbiota was recovered after exposure to benzo[a]pyrene.

Soil type and pH mediated arable soil bacterial compositional variation across geographic distance in North China Plain

A challenge in biogeography is to understand what are the factors and how they regulate soil microbial communities. To explore the coexistence pattern of bacterial community and the factors shaping agricultural soil bacterial community at spatial scale, 135 soil samples were collected from a typically agricultural province in the North China Plain and analyzed with high-throughput 16S rRNA gene sequencing. As expected, bacterial community dissimilarity showed significant distance-decay relationships with 42.2% variation explained by geographic distance and physicochemical factors. Bacterial phyla abundance showed different responses to environmental factors among which soil pH was the primary factor shaping soil bacterial community structure. Bacterial communities in acidic soils suggest lower phylotype richness and phylogenetic diversity and its associated network structure showed greater connectivity and stability compared to those in neutral and alkaline soils. Soil bacterial community diversity was also varied with soil type. Unlike the simplest topological features of co-occurrence network in Cinnamon soil, bacterial community structure was more connected and stable in Lime concretion black soil and Kallotenuales but not the predominant taxa were identified as kinless hub. However, Neisseriales, Anaerolineaceae and Nannocystaceae from Proteobacteria and Chloroflexi with higher relative abundance might support higher levels of ecosystem functions in Fluvo-aquic soil. Taken together, our results suggest that geographic distance and pH variation strongly shaped bacterial community structure with correspondingly diverse co-occurrence patterns observed in different soil pH ranges and types.

Synergistic bioreduction of Te(Ⅳ) using S(0) as electron donor

This study for the first time bioreduced Te(IV) using elemental sulfur (S0) as electron donor, achieving 91.17%±0.8% conversion with reaction rate of 0.77 ± 0.01 mg/L/h in a 60-day cultivation. Characterization using X-ray photoelectron spectroscopy and X-ray power diffraction analyses confirmed that most removed Te(IV) was reduced to elemental Te(0) deposits, while ion chromatogram analysis showed that most S(0) was oxidized to sulfite and sulfate. High-throughput 16S rRNA gene sequencing indicated that the Te(IV) reduction coupled to S(0) oxidation was mediated synergistically by a microbial consortia with S(0)-oxidizing bacteria (Thiobacillus) to generate volatile fatty acids as metabolites and Te(IV)-reducing bacteria (Rhodobacter) to consume formed volatile fatty acids to yield Te(0). The synergy between these two strains presents a novel bioremediation consortium to efficiently treat Te(IV) wastewaters.

Acetate and electricity generation from methane in conductive fiber membrane- microbial fuel cells

Microbial conversion of methane to electricity, fuels, and liquid chemicals has attracted much attention. However, due to the low solubility of methane, it is not considered a suitable substrate for microbial fuel cells (MFCs). In this study, a conductive fiber membrane (CFM) module was constructed as the bioanode of methane-driven MFCs, directly delivering methane. After biofilm formation on the CFM surface, a steady voltage output of 0.6 to 0.7 V was recorded, and the CFM-MFCs obtained a maximum power density of 64 ± 2 mW/m2. Moreover, methane oxidation produced a high concentration of intermediate acetate (up to 7.1 mM). High-throughput 16S rRNA gene sequencing suggests that the microbial community was significantly changed after electricity generation. Methane-related archaea formed a symbiotic consortium with characterized electroactive bacteria and fermentative bacteria, suggesting a combination of three types of microorganisms for methane conversion into acetate and electricity.

A Comparative Study on the Microbial Communities of Rhynchophorus ferrugineus (Red Palm Weevil)-Infected and Healthy Palm Trees

Several studies have investigated palm trees’ microbiota infected with red palm weevil (RPW) (Rhynchophorus ferrugineus), the major pest of palm trees. This study compared the microbial communities of infected and uninfected palm trees in the Hail region, Northern Saudi Arabia, determined by high-throughput 16S rRNA gene sequencing by Illumina MiSeq. The results indicated that taxonomic diversity variation was higher for infected tree trunk than the healthy tree trunk. Soil samples from the vicinity of healthy and infected trees did not have a significant variation in bacterial diversity. Myxococcota, Acidobacteriota, and Firmicutes were the dominant phyla in RPW-infected tree trunk, and Pseudomonadaceae was the most prominent family. This study is the first report on the characterization of RPW-infected and healthy palm trees’ microbiome.

Hypoglycemic effect of astragaloside IV via modulating gut microbiota and regulating AMPK/SIRT1 and PI3K/AKT pathway

Ethnopharmacological relevanceRadix Astragali, the dried root of Astragalus mongholicus Bunge, has long been used in traditional Chinese Medicine to treat diabetes. Astragaloside IV (AS-IV), one of the most active ingredients in the root, has been shown to have anti-diabetes ability; however, its underlying mechanism is still unclear. Materials and methodsIn this study, we evaluated the hypoglycemic effect and possible mechanisms of AS-IV in diabetic mice and insulin resistance-HepG2 cells. The components of the intestinal microflora in mice with type 2 diabetes mellitus (T2DM) were determined using high-throughput 16S rRNA gene sequencing. Moreover, the molecular mechanisms of specific members of insulin signaling pathways were analyzed. ResultsAS-IV significantly reversed the abnormalities in blood lipids, glucose, insulin resistance, as well as oxidative stress levels in T2DM mice. Histological finding showed that AS-IV could protect the cellular architecture of the liver and pancreas. AS-IV also regulated the abundance and diversity of intestinal flora of T2DM mice in a positive direction and increased butyric acid levels. The active role of AS-IV as an anti-diabetic compound by regulating the AMPK/SIRT1 and PI3K/AKT signaling pathways was revealed using a T2DM model and verified through the intervention of inhibitors using insulin-resistance HepG2 cells. ConclusionOur results suggested that AS-IV may be used as an anti-diabetic drug candidate owing to its effects of regulating gut microbiota and AMPK/SIRT1 and PI3K/AKT signaling pathways.

Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age

Understanding the gut microbiota characteristics of endangered species such as the Eurasian otter (Lutra lutra), especially in their early stages of life, could be essential for improving their management and ex situ conservation strategies. Here, we analyzed the gut microbiota diversity, composition, and function of captive Eurasian otters at different ages using high-throughput 16S rRNA gene sequencing. We found that: (1) Clostridiaceae was abundant in all age stages; (2) Lactococcus in cubs is thought to predominate for digesting milk; (3) bacteria associated with amino acid metabolism increase with age, while bacteria associated with carbohydrate metabolism decrease with age, which is likely due to decrease in dietary carbohydrate content (e.g., milk) and increase in dietary protein contents (e.g., fishes) with age; and (4) fish-related bacteria were detected in feces of healthy adults and juveniles. Overall, the gut microbiota of captive Eurasian otters was taxonomically and functionally different by age, which is thought to be attributed to the difference in the diet in their life stages. This study provided baseline information regarding the gut microbiota of Eurasian otters for the first time and contributes to improvement in their management in captivity.

Response of soil bacterial community to agricultural reclamation in the Tengger desert, northwestern China

Given the conditions of scarce soil water availability, high UV exposure and huge temperature fluctuation, plant growth in desert is extremely limited. In the last three decades, reclaiming desertified land for agricultural use via the application of solar greenhouse has been developing in the arid regions, northwestern China. However, the soil microbiome shift driven by the transformation of land use remains largely unexplored. To this end, we examined the diversity and composition of the bacterial community in the vineyard soil at the edge of Tengger desert, using the high-throughput quantitative 16S rRNA gene sequencing. Two types of agricultural managed soils, including those near the plant (PLT) and the others on the fertilization furrow (FTL), were collected. Soils from the open desert land without agricultural practices were used as the control (CON). The results showed that agricultural reclamation significantly (p < 0.05) reduced the desert soil bacterial diversity while promoted the total bacterial abundance from 106 copies up to 108 per ng of DNA, which increased up to 90 folds. Among the dominant bacteria Firmicutes, Proteobacteria, Actinobacteria, and Acidobacteria, Bacilli and Actinobacteria were found to be the keystone taxa responding to the agricultural practices especially to the nutrient inputs from fertilization. The functional prediction of the microbiome suggested that amino acid and carbohydrate transport and metabolism were the most important metabolic pathways differed between the three types of soils. Overall, our findings provide deep insights into the understanding of desert soil microbial responses to agricultural reclamation on the processes of human urbanization and reversion of desertification.