Differences In Bacterial Composition Research Articles

Vegetation as a key driver of the distribution of microbial generalists that in turn shapes the overall microbial community structure in the low Arctic tundra

Understanding the variability of microbial niches and their interaction with abiotic and biotic factors in the Arctic can provide valuable insights into microbial adaptations to extreme environments. This study investigates the structure and diversity of soil bacterial communities obtained from sites with varying vegetation coverage and soil biogeochemical properties in the low Arctic tundra and explores how bacteria interact under different environmental parameters. Our findings reveal differences in bacterial composition and abundance among three bacterial niche breadths (specialists, common taxa, and generalists). Co-occurrence network analysis revealed Rhizobiales and Ktedonobacterales as keystone taxa that connect and support other microbes in the habitat. Low-elevation indicators, such as vascular plants and moisture content, were correlated with two out of three generalist modular hubs and were linked to a large proportion of generalists’ distribution (18%). Structural equation modeling revealed that generalists’ distribution, which influenced the remaining microbial communities, was mainly regulated by vegetation coverage as well as other abiotic and biotic factors. These results suggest that elevation-dependent environmental factors directly influence microbial community structure and module formation through the regulation of generalists’ distribution. Furthermore, the distribution of generalists was mainly affected by macroenvironment filtering, whereas the distribution of specialists was mainly affected by microenvironment filtering (species-engineered microbial niche construction). In summary, our findings highlight the strong top–down control exerted by vegetation on generalists’ distribution, which in turn shapes the overall microbial community structure in the low Arctic tundra.

Characteristics of bacterial community and ARG profiles in the surface and air environments in a spacecraft assembly cleanroom

Understanding the microbial communities and antibiotic resistance genes (ARGs) in spacecraft assembly cleanrooms is crucial for spacecraft microbial control and astronaut safety. However, there have been few reports of ARG profiles and their relationship with microbiomes in such environments. In the present study, we assessed the bacterial community and ARGs in the air dust and surface environments of a typical spacecraft assembly cleanroom. Our results show a significant difference in bacterial composition between surfaces and air dust, as they belong to two distinct ecostates. Bacillus and Acinetobacter were significantly enriched in the air samples. Bacterial community network analysis revealed lower topological parameters and robustness of bacterial networks in the air samples. We also observed different distribution patterns of some typical ARGs between surface and air dust samples. Notably, the ermB gene exhibited a relatively high copy number and was enriched in the surface environment, compared to that in the air. Overall, our study provides insight into the complex microbial community and the distribution and transfer of ARGs in spacecraft assembly cleanrooms, and offers important input for developing control strategies against ARGs.

The microbiota in feces of domestic pigeons in Seoul, Korea

In Korea, feral pigeons pose significant public health risks because they carry various zoonotic pathogens. Human population density is a significant factor in zoonotic disease events. Seoul is one of the largest cities by population density among developed countries and where most of the homeless population in Korea exists. We designed this study to compare the microbiota of pigeon feces by regional characteristics and the presence of homeless individuals. Therefore, this study used 16S rRNA amplicon sequencing to detect possible pathogenic microbes and assess the current risk of zoonosis in Seoul, South Korea. Pigeon fecal samples (n = 144) obtained from 19 public sites (86 and 58 fecal samples from regions in and outside Seoul, respectively) were examined. Potentially pathogenic bacteria were also detected in the fecal samples; Campylobacter spp. was found in 19 samples from 13 regions, Listeriaceae was found in seven samples, and Chlamydia spp. was found in three samples from two regions. Principal coordinates analysis and permutational multivariate analysis of variance revealed a significant difference in bacterial composition between the regions in Seoul (n = 86) and outside Seoul (n = 58) and between the regions with (n = 81) and without (n = 63) homeless individuals. Overall, this study identified various potentially pathogenic microorganisms in pigeon feces at public sites in South Korea. Moreover, this study demonstrates that the microbial composition was influenced by regional characteristics and homelessness. Taken together, this study provides important information for public health strategic planning and disease control.

The microbial composition and functional roles of different kombucha products in Singapore

ABSTRACT Kombucha is a fermented tea known for its health-enhancing properties owing to the bioactive compounds generated by acetic acid bacteria (AAB) and lactic acid bacteria (LAB). We compared the distribution of AAB and LAB across nine kombucha products in Singapore (Product A to I) using shotgun metagenomics. High prevalence of Komagataeibacter species including Komagataeibacter saccharivorans (82.93% in B), Komagataeibacter xylinus (93.38% in D), and Komagataeibacter rhaeticus (92.20% and 30.62% in G and I) was detected in AAB-dominant kombucha. LAB-dominant kombucha was represented mainly by Bacillus coagulans (~99% in E and F) and Lactobacillus nagelii (~60% in H). Despite differences in bacterial composition, all kombucha harbour pathways involved in the biosynthesis of short-chain fatty acids (SCFAs), amino acids and vitamin B12. Interestingly, “fatty acid and beta-oxidation II (peroxisome)” and “fatty acid and beta-oxidation I” were only present in LAB-dominant kombucha. Further study is required to elucidate the significance of the discrepancies.

Effect of two starters (Jiu Yao) on Chinese rice wine microbial community and flavour

SummaryThe starters (Jiu Yao) play key roles in the fermentation of rice wine. However, the microbial composition in the starters and their impact on the dynamic changes in the microbial community during the fermentation of Chinese rice wine (CRW) remain unknown. This study aimed to investigate the microbial community structure in different stages of CRW fermentation with two starters (Q1 and Q2) using high‐throughput sequencing approaches. The β‐diversity analysis showed significant differences in fungal components during fermentation, but no significant differences in bacterial composition. Saccharomyces, Aspergillus, Wickerhamomyces and Hyphopichia were the dominant fungal genera. Pediococcus and Weissella were the main bacterial genera. In addition, the ethanol content of wine fermented with Q1 starter (13.33%) is not as high as that of wine made with Q2 starter (14.57%). The total sugar concentration of Q1 and Q2 starters fermentation broth (HJ‐1 and HJ‐2) is 22.74 and 30.20 g L−1, respectively. The correlation analysis showed 11 dominant microbial genera are strongly related to 27 volatile compounds in HJ‐1, and seven dominant microbial genera are strongly related to 18 volatile compounds in HJ‐2. In conclusion, this study indicated that CRW brewed with different starters have different flavour profiles.

Correlation of the gut microbiome and immune-related adverse events in gastrointestinal cancer patients treated with immune checkpoint inhibitors.

The wide application of immune checkpoint inhibitors has significantly improved the survival expectation of cancer patients. While immunotherapy brings benefits to patients, it also results in a series of immune-related adverse events (irAEs). Increasing evidence suggests that the gut microbiome is critical for immunotherapy response and the development of irAEs. In this prospective study, we recruited 95 patients with advanced/unresectable gastrointestinal cancers treated with immunotherapy and report a comprehensive analysis of the association of the gut microbiome with irAEs. Metagenome sequencing was used to analyze the differences in bacterial composition and metabolic pathways of baseline fecal samples. In summary, we identified bacterial species and metabolic pathways that might be associated with the occurrence of irAEs in gastric, esophageal, and colon cancers. Ruminococcus callidus and Bacteroides xylanisolvens were enriched in patients without severe irAEs. Several microbial metabolic pathways involved in the urea cycle, including citrulline and arginine biosynthesis, were associated with irAEs. We also found that irAEs in different cancer types and toxicity in specific organs and the endocrine system were associated with different gut microbiota profiles. These findings provide the basis for future mechanistic exploration.

Assessing the Effects of Rotifer Feed Enrichments on Turbot (Scophthalmus maximus) Larvae and Post-Larvae Gut-Associated Bacterial Communities

Live feed enrichments are often used in fish larvicultures as an optimized source of essential nutrients to improve larval growth and survival. In addition to this, they may also play an important role in structuring larval-associated microbial communities and may help improve their resistance to diseases. However, there is limited information available on how larval microbial communities and larviculture water are influenced by different live feed enrichments. In the present study, we investigated the effects of two commercial rotifer enrichments (ER) on turbot (Scophthalmus maximus) larval and post-larval gut-associated bacterial communities during larviculture production. We evaluated their effects on bacterial populations related to known pathogens and beneficial bacteria and their potential influence on the composition of bacterioplankton communities during larval rearing. High-throughput 16S rRNA gene sequencing was used to assess the effects of different rotifer enrichments (ER1 and ER2) on the structural diversity of bacterial communities of the whole turbot larvae 10 days after hatching (DAH), the post-larval gut 30 DAH, and the larviculture water. Our results showed that different rotifer feed enrichments were associated with significant differences in bacterial composition of turbot larvae 10 DAH, but not with the composition of larval gut communities 30 DAH or bacterioplankton communities 10 and 30 DAH. However, a more in-depth taxonomic analysis showed that there were significant differences in the abundance of Vibrionales in both 10 DAH larvae and in the 30 DAH post-larval gut fed different RE diets. Interestingly, the ER1 diet had a higher relative abundance of specific amplicon sequence variants (ASVs) related to potential Vibrio-antagonists belonging to the Roseobacter clade (e.g., Phaeobacter and Ruegeria at 10 DAH and Sulfitobacter at 30 DAH). In line with this, the diet was also associated with a lower relative abundance of Vibrio and a lower mortality. These results suggest that rotifer diets can affect colonization by Vibrio members in the guts of post-larval turbot. Overall, this study indicates that live feed enrichments can have modulatory effects on fish bacterial communities during the early stages of development, which includes the relative abundances of pathogenic and antagonist taxa in larviculture systems.

Divergence of epibacterial community assemblage correlates with malformation disease severity in Saccharina japonica seedlings

Malformation disease (MD) is one of the major constraints in the mariculture of the commercially important seaweed Saccharina japonica, which can cause severe losses of the kelp seedlings in the production process. However, the pathogenesis of MD remains largely undetermined. In this study, using cultivation experiments under laboratory conditions, MD severity was estimated for the young sporophytes of S. japonica, which were separately cultivated under different treatment conditions, including light intensity, duration of light exposure, and maturity level of the parent kelp. The associations between MD severity and epibacterial community divergence and assembly patterns were characterized. Higher MD severity significantly correlated with longer light exposure, and with both unmatured and overmatured parent kelp. The bacterial classes γ-Proteobacteria and α-Proteobacteria dominated all samples, but different MD severities were associated with different epibacterial communities. Comparisons of predicted functions for epibacterial communities revealed that longer light exposure led to a depletion in development and regeneration, while overmatured parent kelp resulted in a depletion in glycan biosynthesis and metabolism. Functional comparisons of the epibacterial communities between normal and unmatured parent kelp-generated seedlings revealed significantly different categories related to metabolism, environmental information processing, cellular processes, drug resistance, and bacterial infection. The significantly different pathways between groups, notably those related to bacterial infection and cellular processes, were partly consistent with the differences in bacterial compositions. The assembly of epiphytic bacterial communities was predominately governed by deterministic processes, and less impact was determined when there was significantly higher MD severity except when using overmatured parent kelp. Co-occurrence networks of the epibacterial communities associated with higher MD severity contained fewer nodes and exhibited lower modularity, but had higher graph density and degrees compared with those of seedlings with lower MD severity, indicating more complicated interactions. Nesterenkonia, Glycocaulis, Halomonas, Pseudoalteromonas, Pseudomonas, Loktanella, and Cobetia were frequently determined keystone taxa in communities associated with higher MD severity. The present study enhances our understanding of the factors significantly associated with MD severity and the potential roles of epimicrobiome in determining the disease severity, which will be useful for disease management in the future.

Effects of early-life tosufloxacin tosilate hydrate administration on growth rate, neurobehavior, and gut microbiota at adulthood in male mice.

Reportedly, antibiotics, which are frequently prescribed in children, have long-term effects owing to gut microbiota dysregulation. Tosufloxacin tosilate hydrate (TFLX) is the first orally administered new quinolone with high efficacy and broad-spectrum action approved as an antibacterial agent for pediatric use in Japan. However, studies on the effects of its early-stage administration are limited. Therefore, we aimed to analyze the later effects of its developmental administration by monitoring growth rate, neurobehavior, and gut microbiota in mice. The TFLX was administered via drinking water at a dose of up to 300 mg/kg for two consecutive weeks during the developmental period (4-6 weeks of age) or adulthood (8-10 weeks of age). Thereafter, the body weights of the mice were measured weekly to monitor growth rate. Behavioral tests were also conducted on 11-12-week-old mice to examine the neurobehavioral effects of the treatment. Further, to examine the effects of the treatment on microbiota, fecal samples were collected from the rectum of mice dissected at 12 weeks of age, and 16s rRNA analysis was conducted. Our results showed increased body weights after TFLX administration, without any long-term effects. Behavioral analysis suggested alterations in anxiety-like behaviors and memory recall dysregulation, and gut microbiota analysis revealed significant differences in bacterial composition. These findings indicated that TFLX administration during the developmental period affects mice growth rate, neurobehavior, and gut microbiota structure. This is the first study to report that TFLX is potentially associated with the risk of long effects.

Differences in bacterial composition between vascular epiphyte and parasitic plants living on the same host plants

Abstract. Do HDK, Luqman A, Vu MT, Nguyen HD, Putro YK, Rofiqa EA, Santoso H, Kristanti AN, Hariyanto S, Bui LM, Manuhara YSW, Wibowo AT. 2022. Differences in bacterial composition between vascular epiphyte and parasitic plants living on the same host plants. Biodiversitas 23: 5798-5805. Epiphytic and parasitic plants can grow and complete their life cycle while attached to the host. Therefore, the interactions between these plants and their host provide profound evidence for co-evolution. During these symbiotic interactions, bacteria are actively exchanged between parasitic and epiphytic plants with their hosts. Since epiphytes and parasitic plants have different ways of life, they might assemble their bacterial community differently despite living in the same host. However, direct microbiome comparisons between epiphytic and parasitic plants colonizing the same host have never been evaluated. In this study, we examined the bacterial compositions of the epiphytic Hoya sp. and parasitic Dendrophthoe sp. that grow in two host species, frangipani (Plumeria sp.) and teak (Tectona grandis). The results revealed that bacterial compositions in the root of Hoya sp. are highly similar to the peripheral tissue of the host stem. In contrast, bacterial composition in the haustoria of Dendrophthoe sp. is quite distinct from the host. These results revealed that epiphytes and parasitic plants acquire and assemble their microbiome differently, despite living in the same host species. These differences might originate from different nutrient acquisition strategies between the two plants.

Winogradsky Bioelectrochemical System as a Novel Strategy to Enrich Electrochemically Active Microorganisms from Arsenic-Rich Sediments

Bioelectrochemical systems (BESs) have been extensively studied for treatment and remediation. However, BESs have the potential to be used for the enrichment of microorganisms that could replace their natural electron donor or acceptor for an electrode. In this study, Winogradsky BES columns with As-rich sediments extracted from an Andean watershed were used as a strategy to enrich lithotrophic electrochemically active microorganisms (EAMs) on electrodes (i.e., cathodes). After 15 months, Winogradsky BESs registered power densities up to 650 μWcm-2. Scanning electron microscopy and linear sweep voltammetry confirmed microbial growth and electrochemical activity on cathodes. Pyrosequencing evidenced differences in bacterial composition between sediments from the field and cathodic biofilms. Six EAMs from genera Herbaspirillum, Ancylobacter, Rhodococcus, Methylobacterium, Sphingomonas, and Pseudomonas were isolated from cathodes using a lithoautotrophic As oxidizers culture medium. These results suggest that the tested Winogradsky BES columns result in an enrichment of electrochemically active As-oxidizing microorganisms. A bioelectrochemical boost of centenarian enrichment approaches, such as the Winogradsky column, represents a promising strategy for prospecting new EAMs linked with the biogeochemical cycles of different metals and metalloids.

Gut microbiome diversity of porcine peritonitis model of sepsis

Animal models are essential in understanding of the mechanisms of sepsis moreover the development and the assessment of emerging therapies. In clinically relevant porcine model, however, a significant variability in the host response has been observed among animals. Thus, there is a strong demand to better understand the potential sources of this heterogeneity. In this study, we compared faecal microbiome composition of 12 animals. Three samples were collected at different time points from each animal. Bacteriome was subjected to 16S rDNA profiling. A significant difference in bacterial composition was associated with the season (p < 0.001) but not with the sex of the pig (p = 0.28), the timing of sample collection (p = 0.59), or interactions thereof (all p > 0.3). The season batch explained 55% of the total variance in the bacteriome diversity. The season term was highly significant from the high-resolution level of the bacterial amplicon sequencing variants up to the level of phylum. The diversity of the microbiome composition could significantly influence experimental model of sepsis, and studies are warranted to demonstrate the effects of gut microbiome diversity on the host-response. If confirmed, control of the gut microbiome should become a standard part of the pre-clinical sepsis experiments.

Cholesteatoma has an altered microbiota with a higher abundance of Staphylococcus species.

To compare the microbiota between cholesteatoma and chronic suppurative otitis media (COM) and to identify potential pathogens that explain the relevant phenotypes of cholesteatoma. Prospective cohort study. Surgical specimens collected from 20 cholesteatomas and nine COMs were treated to dissolve biofilms and subjected to 16S ribosomal RNA (rRNA) gene sequencing and amplicon sequence variant-level analysis for microbiota profiling and quantitative comparison. Correlations between the relative abundance of potential pathogens and the volume of the primary resected cholesteatomas were examined. Differences in bacterial composition (beta diversity) were observed between cholesteatomas and COM (p=.002), with a higher abundance of Staphylococcus in cholesteatomas than in COM (p=.005). Common genera in the external auditory canal (EAC) flora, such as Staphylococcus, Corynebacterium, and Cutibacterium, were predominant in both cholesteatoma and COM; Staphylococcus aureus and Pseudomonas aeruginosa were increased in both diseases compared with the EAC flora. Furthermore, coagulase-negative staphylococci (CoNS) were more abundant in cholesteatomas than in COM (p=0.002). Linear discriminant analysis coupled with effect size measurements (LEfSe) identified four CoNS as potential biomarkers for cholesteatoma. The relative abundance of S. aureus, a potential pathogen, was positively correlated with cholesteatoma volume (r= .60, p=.02). The microbiota of cholesteatoma and COM originated from EAC flora, but the bacterial composition was largely altered. Our results suggested that S. aureus infection is involved in cholesteatoma progression. 3b.

Strong Linkage Between Symbiotic Bacterial Community and Host Age and Morph in a Hemipteran Social Insect.

The relationships between symbionts and insects are complex, and symbionts usually have diverse ecological and evolutionary effects on their hosts. The phloem sap-sucking aphids are good models to study the interactions between insects and symbiotic microorganisms. Although aphids usually exhibit remarkable life cycle complexity, most previous studies on symbiotic diversity sampled only apterous viviparous adult females or very few morphs. In this study, high-throughput 16S rDNA amplicon sequencing was used to assess the symbiotic bacterial communities of eleven morphs or developmental stages of the social aphid Pseudoregma bambucicola. We found there were significant differences in bacterial composition in response to different morphs and developmental stages, and for the first time, we revealed male aphids hosted very different symbiotic composition featured with low abundance of dominant symbionts but high diversity of total symbionts. The relative abundance of Pectobacterium showed relatively stable across different types of samples, while that of Wolbachia fluctuated greatly, indicating the former may have a consistent function in this species and the latter may provide specific function for certain morphs or developmental stages. Our study presents new evidence of complexity of symbiotic associations and indicates strong linkage between symbiotic bacterial community and host age and morph.

Evaluation of constructed wetland systems toward naturalization of the elemental composition and microbial community in wastewater treatment plant effluent

Numerous studies have been conducted on the advanced treatment of wastewater treatment plant (WWTP) effluent by constructed wetlands (CWs); however, no studies have focused on the effect of the naturalization function of CWs on WWTP tailwater, i.e., reducing imbalances in the elemental composition and microbial community, compared with natural surface water (NSW). Therefore, the possible naturalization functions of CWs were evaluated by comparing the elemental composition, microbial structure and function in NSW with the influent and effluent of CW. Surveys were conducted in seventeen full-scale wetlands constructed to treat WWTP tailwater in eastern China, and the largest lake in the region, Taihu Lake, was selected as the reference for NSW. The imbalance index (IMI) was proposed to characterize the difference in the elemental proportions between tailwater and the references. The results showed that the IMI values for the WWTP effluent ranged from 0.51 to 0.10 and from 0.95 to 0.37 for macroelements and microelements, with average values of 0.30 and 0.62, respectively. When macronutrient IMI>0.27 or micronutrient IMI>0.43, the CWs alleviated the element imbalance; otherwise, the CWs increased the IMI and aggravated the imbalance. With the Hoagland formula as the reference, a similar result was obtained. CW treatment reduced the difference in bacterial composition between tailwater and NSW. According to FAPROTAX and BugBase function prediction, CW treatment reduced the difference in the relative abundance of microbial functions related to C, N, and S cycles, pathogenicity and antibiotic resistance genes between tailwater and NSW. The CW area and hydraulic retention time were significantly positively correlated with the naturalization index. Therefore, the CW system can naturalize tailwater in terms of both elemental composition and microbial composition and function, indicating the necessity of re-evaluating CW functions in treating WWTP tailwater.

Identifying the difference in bacterial composition and life history strategies between high versus low nutrient soils

In this study, we aim to identify bacterial composition in soils treated with and without wood chips, as well as high levels and low levels of nitrogen. In order to do this, we used both culture dependent methods including plating, observing, and GenIII plates; as well as culture independent methods which include microbiome sequencing and EcoPlates. By doing this, we concluded that the bacterial communities differ between unamended and wood-chipped treated soils. Multiple differences were identified: rate of carbon consumption, bacterial diversity, rRNA gene copy number, and colony morphologies. Identifying the bacteria in wood-chipped soils will allow us to understand their effect on biogeochemical cycles, plant pathogens, and relationship with the trees (symbiotic/pathogen). Additionally, understanding the effect lower nitrogen levels have on the bacterial composition of soils can lead to reduction of synthetic fertilizer use, therefore lessening the environmental impact of nitrogen.

Different feeding strategies can affect growth performance and rumen functions in Gangba sheep as revealed by integrated transcriptome and microbiome analyses.

Due to the harsh environment in the Tibetan Plateau, traditional grazing greatly limits the growth potential of local animals and causes severe ecosystem degradation. This is an urgent issue to be solved, which requires alternative strategies for grazing animals in the Tibetan alpine pastoral livestock systems. This study aimed to investigate the effects of different feeding strategies on growth performance and ruminal microbiota-host interactions in the local breed of sheep (Gangba sheep). Thirty 9-month old Gangba sheep (n = 10 per group) were assigned to natural grazing (G), semi-grazing with supplementation (T), and barn feeding (F) groups (supplementation of concentrate and oat hay) based on body weight. At the end of the experiment (75 d), all sheep were weighed, rumen fluid was obtained from six sheep per group, and ruminal epithelium was obtained from 3 sheep per group. The results showed that: (1) Compared with the G and T groups, the F group significantly increased dry matter intake, average daily gain, and feed conversion ratio of animals. Additionally, Gangba sheep in the F group had higher concentrations of ruminal short-chain volatile fatty acids (VFAs), especially propionate and butyrate (P <0.05) than sheep in the G and T groups. (2) The principal coordinates analysis indicated a significant difference in bacterial composition among different feed strategies. More specifically, the relative abundance of propionate (unidentified F082 and Succiniclasticum) and butyrate-producing (Eubacterium_coprostanoligenes_group) genera were also observed to be increased in the F group, in which unidentified F082 was identified as a differential biomarker among the three groups according to linear discriminant analysis effect size analysis. (3) The dynamics of the rumen epithelial transcriptome revealed that ECM-receptor interactions, focal adhesion, and PI3K-Akt signaling pathways, which are critical in mediating many aspects of cellular functions such as cell proliferation and motility, were upregulated in the F group. In conclusion, under harsh conditions in the Tibetan alpine meadow, barn feeding increased ruminal VFAs concentrations (especially propionate and butyrate), which stimulated gene expression related to cell proliferation in rumen epithelium, appearing to be superior to natural grazing and semi-grazing in gaining body weight of the local Gangba sheep.

Deciphering Resistome in Patients With Chronic Obstructive Pulmonary Diseases and Clostridioides difficile Infections.

Antibiotics alter the gut microbiome and cause dysbiosis leading to antibiotic-resistant organisms. Different patterns of antibiotic administration cause a difference in bacterial composition and resistome in the human gut. We comprehensively investigated the association between the distribution of antibiotic resistance genes (ARGs), bacterial composition, and antibiotic treatments in patients with chronic obstructive pulmonary diseases (COPD) and Clostridioides difficile infections (CDI) who had chronic or acute intermittent use of antibiotics and compared them with healthy individuals. We analyzed the gut microbiomes of 61 healthy individuals, 16 patients with COPD, and 26 patients with CDI. The COPD patients were antibiotic-free before stool collection for a median of 40 days (Q1: 9.5; Q3: 60 days), while the CDI patients were antibiotic-free for 0 days (Q1: 0; Q3: 0.3). The intra-group beta diversity measured by the median Bray-Curtis index was the lowest for the healthy individuals (0.55), followed by the COPD (0.69) and CDI groups (0.72). The inter-group beta diversity was the highest among the healthy and CDI groups (median index = 0.89). The abundance of ARGs measured by the number of reads per kilobase per million reads (RPKM) was 684.2; 1,215.2; and 2,025.1 for the healthy, COPD, and CDI groups. It was negatively correlated with the alpha diversity of bacterial composition. For the prevalent ARG classes, healthy individuals had the lowest diversity and abundance of aminoglycoside, β-lactam, and macrolide-lincosamide-streptogramin (MLS) resistance genes, followed by the COPD and CDI groups. The abundances of Enterococcus and Escherichia species were positively correlated with ARG abundance and the days of antibiotic treatment, while Bifidobacterium and Ruminococcus showed negative correlations for the same. In addition, we analyzed the mobilome patterns of aminoglycoside and β-lactam resistance gene carriers using metagenomic sequencing data. In conclusion, the ARGs were significantly enhanced in the CDI and COPD groups than in healthy individuals. In particular, aminoglycoside and β-lactam resistance genes were more abundant in the CDI and COPD groups, but the dominant mobile genetic elements that enable the transfer of such genes showed similar prevalence patterns among the groups.

Microbial communities in crude oil phase and filter-graded aqueous phase from a Daqing oilfield after polymer flooding.

The aim was to characterize indigenous micro-organisms in oil reservoirs after polymer flooding (RAPF). The microbial communities in the crude oil phase (Oil) and in the filter-graded aqueous phases Aqu0.22 (>0.22 μm) and Aqu0.1 (0.1-0.22 μm) were investigated by 16S rRNA gene high-throughput sequencing. Indigenous micro-organisms related to hydrocarbon degradation prevailed in the three phases of each well. However, obvious differences in bacterial compositions were observed amongst the three phases of the same well and amongst the same phase of different wells. The crude oil and Aqu0.22 shared many dominant bacteria. Aqu0.1 contained a unique bacterial community in each well. Most bacteria in Aqu0.1 were affiliated to culturable genera, suggesting that they may adapt to the oil reservoir environment by reduction of cell size. Contrary to the bacterial genera, archaeal genera were similar in the three phases but varied in relative abundances. The observed microbial differences may be driven by specific environmental factors in each oil well. The results suggest an application potential of microbial enhanced oil recovery (MEOR) technology in RAPF. The crude oil and Aqu0.1 contain many different functional micro-organisms related to hydrocarbon degradation. Both should not be overlooked when investing and exploring the indigenous micro-organisms for MEOR. This work facilitates the understanding of microbial community structures in RAPF and provides information for microbial control in oil fields.

Alteration of Skin Microbiome in CKD Patients Is Associated With Pruritus and Renal Function.

Dysbiotic gut microbiome in chronic kidney disease (CKD) patients has been extensively explored in recent years. Skin microbiome plays a crucial role in patients with skin diseases or even systemic disorders. Pruritus is caused by the retention of uremic solutes in the skin. Until now, no studies have investigated the role of skin microbiome in CKD and its association with pruritus. Here, we aim to examine the bacterial profile of skin microbiome in CKD and whether it is correlated to pruritus. A total of 105 CKD patients and 38 healthy controls (HC) were recruited. Skin swab was used to collect skin samples at the antecubital fossa of participants. Bacterial 16S rRNA genes V3–V4 region was sequenced on NovaSeq platform. On the day of skin sample collection, renal function was assessed, and numeric rating scale was used to measure pruritus severity. Principal coordinate analysis (PCoA) revealed a significant difference in bacterial composition between the groups of CKD and HC. A depletion of bacterial diversity was observed in CKD patients. Akkermansia, Albimonas, Escherichia–Shigella, etc. showed significant higher abundance in CKD patients, whereas Flavobacterium, Blastomonas, Lautropia, etc. significantly declined in patients. Escherichia–Shigella achieved an acceptable diagnostic biomarker with area under the curve (AUC) value of 0.784 in the receiver operating characteristics (ROC) curve. In addition, CKD patients with pruritus (P-CKD) had a different bacterial community comparing to those without pruritus (non-P-CKD) and HC group. Several bacterial genera showing significant difference between P-CKD and non-P-CKD/HC, such as Oribacterium, significantly declined in P-CKD patients than that in the HC group, and Methylophaga significantly increased in P-CKD patients compared to that in HC subjects. Escherichia–Shigella was positively associated with the levels of pruritus severity, blood urea nitrogen (BUN), uric acid, and urine protein; Oribacterium was negatively associated with pruritus severity, whereas it was positively associated with estimated glomerular filtration rate (eGFR) and 24-h urine volume. The dysbiotic of skin microbiome in CKD patients and its association with pruritus and renal function shed a light on skin probiotics.