Bacterial Microbiome Research Articles

Biotic countermeasures that rescue Nannochloropsis gaditana from a Bacillus safensis infection.

The natural assemblage of a symbiotic bacterial microbiome (bacteriome) with microalgae in marine ecosystems is now being investigated as a means to increase algal productivity for industry. When algae are grown in open pond settings, biological contamination causes an estimated 30% loss of the algal crop. Therefore, new crop protection strategies that do not disrupt the native algal bacteriome are needed to produce reliable, high-yield algal biomass. Bacteriophages offer an unexplored solution to treat bacterial pathogenicity in algal cultures because they can eliminate a single species without affecting the bacteriome. To address this, we identified a highly virulent pathogen of the microalga Nannochloropsis gaditana, the bacterium Bacillus safensis, and demonstrated rescue of the microalgae from the pathogen using phage. 16S rRNA amplicon sequencing showed that phage treatment did not alter the composition of the bacteriome. It is widely suspected that the algal bacteriome could play a protective role against bacterial pathogens. To test this, we compared the susceptibility of a bacteriome-attenuated N. gaditana culture challenged with B. safensis to a N. gaditana culture carrying a growth-promoting bacteriome. We showed that the loss of the bacteriome increased the susceptibility of N. gaditana to the pathogen. Transplanting the microalgal bacteriome to the bacteriome-attenuated culture reconstituted the protective effect of the bacteriome. Finally, the success of phage treatment was dependent on the presence of beneficial bacteriome. This study introduces two synergistic countermeasures against bacterial pathogenicity in algal cultures and a tractable model for studying interactions between microalgae, phages, pathogens, and the algae microbiome.

Community structure and niche differentiation of endosphere bacterial microbiome in Camellia oleifera.

Understanding the changes in bacterial community structure in different microenvironments of Camellia oleifera is essential to better explore the benign interaction between beneficial microorganisms and plants. Using Camellia oleifera trees, a Chinese wooden oil plant as a model ecosystem, we characterized the archaeal and bacterial microbiome across five different tissue-level niches using 16S rRNA gene analyses. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. The species replacement process (69.90%) is the dominant factor in the differences in bacterial community structure. The dominant bacteria phyla (Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia) of Camellia oleifera show a significant plant compartment (roots, stems, leaves, fruits) enrichment effects. A variety of bacteria (Hymenobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Mesorhizobium, Bradyrhizobium, Bacillus, Ochrobactrum, Pantoea, Pseudomonas, etc.) with nitrogen-fixed potentials are enriched in Camellia oleifera tissue. In addition, the hub bacterial groups of Camellia oleifera are Nitrospira, Haemophilus, Staphylococcus, Ruminiclostridium, and Ochrobactrum. They are widespread colonization in various tissues with a low relative abundance and may play an important role in the nitrogen cycle, host life promotion, and plant defense. This study provides a holistic understanding of the endosphere bacterial community structure, which is one of the most complete ecological niche-level analyses of Camellia oleifera. These results provide a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.IMPORTANCEMicroorganisms inhabited various tissues of plants and play a key role in promoting plant growth, nutritional absorption, and resistance. Our research indicates that the diversity of Camellia oleifera endophytic bacterial communities is highly dependent on the plant compartment. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Chloroflexi, and Verrucomicrobia are dominant bacteria phyla. The tissues of Camellia oleifera contain various bacteria with nitrogen fixation potential, host life promotion, and plant defense. This study provides a scientific theoretical basis for an in-depth discussion of plant-endosphere microbial interaction and better exploration of benign interaction of beneficial microorganisms and plants.

Inhaler Steroid Use Changes Oral and Airway Bacterial and Fungal Microbiome Profile in Asthma Patients

Introduction: The full spectrum of bacterial and fungal species in adult asthma and the effect of inhaled corticosteroid use is not well described. The aim was to collect mouthwash and induced sputum samples from newly diagnosed asthma patients in the pretreatment period and in chronic asthma patients while undergoing regular maintenance inhaled corticosteroid therapy, in order to demonstrate the bacterial and fungal microbiome profile. Methods: The study included 28 asthmatic patients on inhaler steroid therapy, 25 steroid-naive asthmatics, and 24 healthy controls. Genomic DNA was isolated from induced sputum and mouthwash samples. Analyses were performed using bacterial primers selected from the 16S rRNA region for the bacterial genome and “panfungal” primers selected from the 5.8S rRNA region for the fungal genome. Results: Dominant genera in mouthwash samples of steroid-naive asthmatics were Neisseria, Haemophilus, and Rothia. The oral microbiota of asthmatic patients on inhaler steroid treatment included Neisseria, Rothia, and Veillonella species. Abundant genera in induced sputum samples of steroid-naive asthma patients were Actinomyces, Granulicatella, Fusobacterium, Peptostreptococcus, and Atopobium. Sputum microbiota of asthma patients taking inhaler steroids were dominated by Prevotella and Porphyromonas. Mucor plumbeus and Malassezia restricta species were abundant in the airways of steroid-naive asthma patients. Choanephora infundibulifera and Malassezia restricta became dominant in asthma patients taking inhaled steroids. Conclusion: The oral and airway microbiota consist of different bacterial and fungal communities in healthy and asthmatic patients. Inhaler steroid use may influence the composition of the oral and airway microbiota.

Microbiome of infected fracture nonunion: Does it affect outcomes?

BackgroundInfected fracture nonunions often require prolonged treatment and recovery courses. It is unclear whether the bacterial microbiome influences the time to healing as well as the eradication of infection. The goals of this study are (1) to assess the bacterial microbiome affecting infected nonunions and (2) to evaluate the effects of bacterial speciation on associated outcomes. MethodsBetween 2006 and 2022, data from 551 adult patients from a single academic institution who presented with a fracture nonunion were analyzed retrospectively for infection. All patients underwent revision surgery with three sets of cultures obtained intra-operatively. Patients with significant intra-operative cultures were grouped into gram-positive and gram-negative culture cohorts. These patients were managed with a standardized protocol involving surgical debridement, nonunion site fixation, and culture-directed antibiotic treatment. Primary outcome was time to fracture union. Secondary outcomes included number of re-operations and eventual amputation or reconstructive surgery. Results56 nonunion patients (10 %) were diagnosed with an infected nonunion (44 g-positive, 12 g-negative). Of these, 3 g-positive patients received an amputation or arthroplasty procedure prior to fracture union, and seven were lost to follow-up. There were no significant differences in age, gender, or nonunion site between cohorts. Most nonunions occurred in the lower extremity. The most common bacteria were staph species (54.3 %). 36 g-positive and 10 g-negative patients achieved fracture union. Time to union was on average 158.4 days longer in the gram-negative cohort—but did not reach statistical significance (446.8 days gram-positive, 662.3 days gram-negative, p = 0.69). There was no difference in re-operation rates (1.9 % gram-positive, 2.2 % gram-negative, p = 0.84). ConclusionsPatients with infected nonunions had wide-ranging bacterial contamination that were treated successfully using a standardized protocol. However, patients with any gram-negative culture trended toward a delay in time to union.

Diversity and structure of the root-associated bacterial microbiomes of four mangrove tree species, revealed by high-throughput sequencing.

Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. At present, most of our understanding of mangrove root-related microbial diversity is obtained from specific mangrove species in selected geographic regions. Relatively little is known about the composition of the bacterial microbiota existing in disparate mangrove species microenvironments, particularly the relationship among different mangrove species in tropical environments. We collected the root, rhizosphere soil, and non-rhizosphere soil of four mangrove trees (Acanthus ilicifolius, Bruguiera gymnorrhiza, Clerodendrum inerme, and Lumnitzera racemosa) and detected the 16S rRNA gene by a conventional PCR. We performed high throughput sequencing using Illumina Novaseq 6000 platform (2×250 paired ends) to investigate the bacterial communities related with the different mangrove species. We analyzed the bacterial diversity and composition related to the diverse ecological niches of mangrove species. Our data confirmed distinct distribution patterns of bacterial communities in the three rhizocompartments of the four mangrove species. Microbiome composition varied with compartments and host mangrove species. The bacterial communities between the endosphere and the other two compartments were distinctly diverse independent of mangrove species. The large degree of overlap in critical community members of the same rhizocompartment across distinct mangrove species was found at the phylum level. Furthermore, this is the first report of Acidothermus found in mangrove environments. In conclusion, understanding the complicated host-microbe associations in different mangrove species could lay the foundation for the exploitation of the microbial resource and the production of secondary metabolites.

Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities.

Terpenes are among the oldest and largest class of plant-specialized bioproducts that are known to affect plant development, adaptation, and biological interactions. While their biosynthesis, evolution, and function in aboveground interactions with insects and individual microbial species are well studied, how different terpenes impact plant microbiomes belowground is much less understood. Here we designed an experiment to assess how belowground exogenous applications of monoterpenes (1,8-cineole and linalool) and a sesquiterpene (nerolidol) delivered through an artificial root system impacted its belowground bacterial and fungal microbiome. We found that the terpene applications had significant and variable impacts on bacterial and fungal communities, depending on terpene class and concentration; however, these impacts were localized to the artificial root system and the fungal rhizosphere. We complemented this experiment with pure culture bioassays on responsive bacteria and fungi isolated from the sorghum rhizobiome. Overall, higher concentrations (200 µM) of nerolidol were inhibitory to Ferrovibrium and tested Firmicutes. While fungal isolates of Penicillium and Periconia were also more inhibited by higher concentrations (200 µM) of nerolidol, Clonostachys was enhanced at this higher level and together with Humicola was inhibited by the lower concentration tested (100 µM). On the other hand, 1,8-cineole had an inhibitory effect on Orbilia at both tested concentrations but had a promotive effect at 100 µM on Penicillium and Periconia. Similarly, linalool at 100 µM had significant growth promotion in Mortierella, but an inhibitory effect for Orbilia. Together, these results highlight the variable direct effects of terpenes on single microbial isolates and demonstrate the complexity of microbe-terpene interactions in the rhizobiome. IMPORTANCE Terpenes represent one of the largest and oldest classes of plant-specialized metabolism, but their role in the belowground microbiome is poorly understood. Here, we used a "rhizobox" mesocosm experimental set-up to supply different concentrations and classes of terpenes into the soil compartment with growing sorghum for 1 month to assess how these terpenes affect sorghum bacterial and fungal rhizobiome communities. Changes in bacterial and fungal communities between treatments belowground were characterized, followed by bioassays screening on bacterial and fungal isolates from the sorghum rhizosphere against terpenes to validate direct microbial responses. We found that microbial growth stimulatory and inhibitory effects were localized, terpene specific, dose dependent, and transient in time. This work paves the way for engineering terpene metabolisms in plant microbiomes for improved sustainable agriculture and bioenergy crop production.

Plant neopolyploidy and genetic background differentiate the microbiome of duckweed across a variety of natural freshwater sources.

Whole-genome duplication has long been appreciated for its role in driving phenotypic novelty in plants, often altering the way organisms interface with the abiotic environment. Only recently, however, have we begun to investigate how polyploidy influences interactions of plants with other species, despite the biotic niche being predicted as one of the main determinants of polyploid establishment. Nevertheless, we lack information about how polyploidy affects the diversity and composition of the microbial taxa that colonize plants, and whether this is genotype-dependent and repeatable across natural environments. This information is a first step towards understanding whether the microbiome contributes to polyploid establishment. We, thus, tested the immediate effect of polyploidy on the diversity and composition of the bacterial microbiome of the aquatic plant Spirodela polyrhiza using four pairs of diploids and synthetic autotetraploids. Under controlled conditions, axenic plants were inoculated with pond waters collected from 10 field sites across a broad environmental gradient. Autotetraploids hosted 4%-11% greater bacterial taxonomic and phylogenetic diversity than their diploid progenitors. Polyploidy, along with its interactions with the inoculum source and genetic lineage, collectively explained 7% of the total variation in microbiome composition. Furthermore, polyploidy broadened the core microbiome, with autotetraploids having 15 unique bacterial taxa in addition to the 55 they shared with diploids. Our results show that whole-genome duplication directly leads to novelty in the plant microbiome and importantly that the effect is dependent on the genetic ancestry of the polyploid and generalizable over many environmental contexts.

The Influence of Oral Terbinafine on Gut Fungal Microbiome Composition and Microbial Translocation in People Living with HIV Treated for Onychomycosis.

People living with HIV (PLWH) display altered gut epithelium that allows for the translocation of microbial products, contributing to systemic immune activation. Although there are numerous studies which examine the gut bacterial microbiome in PLWH, few studies describing the fungal microbiome, or the mycobiome, have been reported. Like the gut bacterial microbiome, the fungal microbiome and its by-products play a role in maintaining the body's homeostasis and modulating immune function. We conducted a prospective study to assess the effects of oral terbinafine, an antifungal agent widely used against onychomycosis, on gut permeability and microbiome composition in ART-treated PLWH (trial registration: ChiCTR2100043617). Twenty participants completed all follow-up visits. During terbinafine treatment, the levels of the intestinal fatty acid binding protein (I-FABP) significantly increased, and the levels of interleukin-6 (IL-6) significantly decreased, from baseline to week 12. Both markers subsequently returned to pre-treatment levels after terbinafine discontinuation. After terbinafine treatment, the abundance of fungi decreased significantly, while the abundance of the bacteria did not change. After terbinafine discontinuation, the abundance of fungi returned to the levels observed pre-treatment. Moreover, terbinafine treatment induced only minor changes in the composition of the gut bacterial and fungal microbiome. In summary, oral terbinafine decreases fungal microbiome abundance while only slightly influencing gut permeability and microbial translocation in ART-treated PLWH. This study's findings should be validated in larger and more diverse studies of ART-treated PLWH; our estimates of effect size can be used to inform optimal sample sizes for future studies.

Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean.

Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.

Evidence supportive of a bacterial component in the etiology for Alzheimer's disease and for a temporal-spatial development of a pathogenic microbiome in the brain.

Over the last few decades, a growing body of evidence has suggested a role for various infectious agents in Alzheimer's disease (AD) pathogenesis. Despite diverse pathogens (virus, bacteria, fungi) being detected in AD subjects' brains, research has focused on individual pathogens and only a few studies investigated the hypothesis of a bacterial brain microbiome. We profiled the bacterial communities present in non-demented controls and AD subjects' brains. We obtained postmortem samples from the brains of 32 individual subjects, comprising 16 AD and 16 control age-matched subjects with a total of 130 samples from the frontal and temporal lobes and the entorhinal cortex. We used full-length 16S rRNA gene amplification with Pacific Biosciences sequencing technology to identify bacteria. We detected bacteria in the brains of both cohorts with the principal bacteria comprising Cutibacterium acnes (formerly Propionibacterium acnes) and two species each of Acinetobacter and Comamonas genera. We used a hierarchical Bayesian method to detect differences in relative abundance among AD and control groups. Because of large abundance variances, we also employed a new analysis approach based on the Latent Dirichlet Allocation algorithm, used in computational linguistics. This allowed us to identify five sample classes, each revealing a different microbiota. Assuming that samples represented infections that began at different times, we ordered these classes in time, finding that the last class exclusively explained the existence or non-existence of AD. The AD-related pathogenicity of the brain microbiome seems to be based on a complex polymicrobial dynamic. The time ordering revealed a rise and fall of the abundance of C. acnes with pathogenicity occurring for an off-peak abundance level in association with at least one other bacterium from a set of genera that included Methylobacterium, Bacillus, Caulobacter, Delftia, and Variovorax. C. acnes may also be involved with outcompeting the Comamonas species, which were strongly associated with non-demented brain microbiota, whose early destruction could be the first stage of disease. Our results are also consistent with a leaky blood-brain barrier or lymphatic network that allows bacteria, viruses, fungi, or other pathogens to enter the brain.

Alterations of the bacterial ocular surface microbiome are found in both eyes of horses with unilateral ulcerative keratitis.

Next generation sequencing (NGS) studies in healthy equine eyes have shown a more diverse ocular surface microbiota compared to culture-based techniques. This study aimed to compare the bacterial ocular surface microbiota in both eyes of horses with unilateral ulcerative keratitis (UK) with controls free of ocular disease. Conjunctival swabs were obtained from both ulcerated eyes and unaffected eyes of 15 client-owned horses with unilateral UK following informed consent, as well as from one eye of 15 healthy horses. Genomic DNA was extracted from the swabs and sequenced on an Illumina platform using primers that target the V4 region of bacterial 16S rRNA. Data were analyzed using Quantitative Insights Into Molecular Ecology (QIIME2). The ocular surface of ulcerated eyes had significantly decreased species richness compared with unaffected fellow eyes (Chao1 q = 0.045, Observed ASVs p = 0.045) with no differences in evenness of species (Shannon q = 0.135). Bacterial community structure was significantly different between either eye of horses with UK and controls (unweighted UniFrac: control vs. unaffected, p = 0.03; control vs. ulcerated, p = 0.003; unaffected vs. ulcerated, p = 0.016). Relative abundance of the gram-positive taxonomic class, Bacilli, was significantly increased in ulcerated eyes compared with controls (q = 0.004). Relative abundance of the taxonomic family Staphylococcaceae was significantly increased in ulcerated and unaffected eyes compared with controls (q = 0.030). The results suggest the occurrence of dysbiosis in infected eyes and reveal alterations in beta diversity and taxa of unaffected fellow eyes. Further investigations are necessary to better understand the role of the microbiome in the pathophysiology of ocular surface disease.

Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods.

Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.

Effects of Phlorotannins from Sargassum on In Vitro Rumen Fermentation, Microbiota and Fatty Acid Profile.

The fatty acid profiles of ruminant-derived products are closely associated with human health. Ruminal microbiota play a vital role in modulating rumen biohydrogenation (BH). The aim of this study was to assess the influence of dietary supplementation with phlorotannins (PTs) extracted from Sargassum on rumen fermentation, fatty acid composition and bacterial communities by an in vitro culture study. The inclusion of PTs in the diet increased dry matter digestibility and gas production, and reduced ammonia-N concentration and pH. PT extract inhibited rumen BH, increasing the content of trans-9 C18:1, cis-9 C18:1, trans-9 and trans-12 C18:2 and reducing C18:0 concentration. 16S rRNA sequencing revealed that PTs caused an obvious change in rumen bacterial communities. The presence of Prevotella decreased while carbohydrate-utilizing bacteria such as Prevotellaceae_UCG-001, Ruminococcus, Selenomonas, Ruminobacter and Fibrobacter increased. Correlation analysis between rumen FA composition and the bacterial microbiome revealed that Prevotellaceae_UCG-001, Anaerovorax, Ruminococcus, Ruminobacter, Fibrobacter, Lachnospiraceae_AC2044_group and Clostridia_UCG-014 might have been involved in the BH process. In conclusion, the results suggest that the inclusion of PTs in the diet improved rumen fermentation and FA composition through modulating the rumen bacterial community.

The gut microbiome changes in wild type and IL-18 knockout mice after 9.0 Gy total body irradiation

BackgroundRecent studies have shown that gut microbiome plays important roles in response to radiation exposure. IL-18, an inflammatory cytokine, is highly elevated in mice, mini-pigs and nonhuman primates after radiation exposure. Blocking IL-18 using its endogenous binding protein (IL-18BP) increases mice survival after radiation exposure by decreasing bone marrow interferon-gamma levels.MethodsTo further characterize the roles of IL-18 in response to radiation, both wild type and IL-18 knockout (IL-18 KO) mice were exposed to 9.0 Gy total body irradiation (TBI). The 30-day survival result demonstrated that IL-18 KO mice were significantly more resistant to radiation compared to the wild type mice (p < 0.0001). Mouse faecal samples were collected at pre-radiation (d0), d1, d3, d7, d14, d21 and d29 after radiation exposure. Microbiome profiling was performed on the faecal samples using 16S and ITS sequencing technology.ResultsData analysis showed that there was significant difference in the bacterial microbiome between wild type and IL-18 KO mice. Cohousing of wild type and IL-18 KO mice decreased the bacterial microbiome difference between the two genotypes. Much fewer bacterial genera were significantly changed in wild type mice than the IL-18 KO mice after radiation exposure. The different composition of the IL-18 KO mice and wild type mice persisted even after radiation exposure. Bacterial genera that significantly correlated with other genera were identified in the IL-18 KO and wild type mice. The metabolic pathways that differentially expressed in both genotypes were identified. The animal bacterial microbiome data could be used to predict the animal’s radiation status. The fungal microbiome had no significant difference regarding genotype or time after radiation exposure.ConclusionThe current study helps understand the gut microbiome in different genetic backgrounds and its temporal changes after radiation exposure. Our data provide insight into the mechanisms underlying radiation-induced toxicity and help identify bacteria important in response to radiation.

Ingestion and biodegradation of disposable surgical masks by yellow mealworms Tenebrio molitor larvae: Differences in mask layers and effects on the larval gut microbiome

During the COVID-19 pandemic, the usage and production of face masks considerably increased, resulting in large quantities of mask waste accumulating in the natural environment. To investigate whether masks of polypropylene (PP) material could be ingested and degraded by insect worms like PP foam plastic, yellow mealworms were provided with different layers of disposable surgical masks as sole diets for 30 d. Although mask layers, especially the middle layer of melt-blown filter, could be ingested by yellow mealworms, sole mask layer diets had adverse effects on the larval survival and growth. Analyses of Fourier transform infrared spectroscopy, differential scanning calorimeter and thermogravimetric, and gel permeation chromatography demonstrated the changes of functional groups, thermostability and molecular weights in frass compared to original masks, indicating the partial oxidation and degradation of masks. And the depolymerization of the middle layer of masks by yellow mealworms was different from that of other layers. The larval gut bacterial and fungal microbiomes were assessed by Illumina MiSeq, indicating that both of them shifted upon sole layer mask diets. Changes in relative abundances of dominant bacterial and fungal genera demonstrated the strong association between gut microbiome and mask degradation. For instance, unclassified Enterobacteriaceae was closely associated with outer layers degradation. Lactococcus and unclassified Ascomycota were responsible for middle layers degradation, while Lactococcus and Morganella for inner layers degradation. In conclusion, disposable surgical masks of PP material could be ingested and biodegraded by yellow mealworms. The diversities of gut bacterial and fungal microbiomes were associated with the differences in rigid crystalline structures of the layer masks.

A prebiotic diet modulates the oral microbiome composition and results in the attenuation of oropharyngeal candidiasis in mice.

Oral bacteria can influence the ability of Candida albicans to cause oropharyngeal candidiasis (OPC). We recently reported that a Lactobacillus johnsonii-enriched oral microbiota reduced C. albicans virulence in an immunosuppressed OPC mouse model. As a follow-up, in this work, we aimed to enrich the resident oral Lactobacillus communities with a prebiotic diet to further assess their effect on the severity of OPC. We tested the effect of a prebiotic xylo-oligosaccharides (XOS)-enriched diet in the oral global bacterial composition and severity of OPC. We assessed changes in the oral microbiome composition via 16S-rRNA gene high-throughput sequencing, validated by qPCR. The impact of the prebiotic diet on Candida infection was assessed by quantifying changes in oral fungal and bacterial biomass and scoring tongue lesions. Contrary to expectations, oral Lactobacillus communities were not enriched by the XOS-supplemented diet. Yet, XOS modulated the oral microbiome composition, increasing Bifidobacterium abundance and reducing enterococci and staphylococci. In the OPC model, the XOS diet attenuated Candida virulence and bacterial dysbiosis, increasing lactobacilli and reducing enterococci on the oral mucosa. We conclude that XOS attenuates Candida virulence by promoting a bacterial microbiome structure more resilient to Candida infection. IMPORTANCE This is the first study on the effects of a prebiotic diet on the oral mucosal bacterial microbiome and an oropharyngeal candidiasis (OPC) mouse model. We found that xylo-oligosaccharides change the oral bacterial community composition and attenuate OPC. Our results contribute to the understanding of the impact of the oral bacterial communities on Candida virulence.

Composition of bacterial microbiome in sputum of patients with localized forms of pulmonary tuberculosis

Recent studies have shown that the respiratory bacterial microbiome has an impact on the development of pulmonary tuberculosis. Changes in the composition of the microbiome have been associated with the pathogenesis of Mycobacterium tuberculosis infection, response to therapy, and clinical outcomes of the disease. To date, the composition of the respiratory microbiome has not been studied in patients with localized forms of pulmonary tuberculosis. Methods. In the present study, the taxonomic composition of the sputum microbiome of 14 patients with localized forms of pulmonary tuberculosis (tuberculomas) and 14 healthy donors in the comparison group was analyzed by sequencing (NGS) of the V3 – V4 region of the bacterial gene encoding 16S rRNA. Results. The sputum microbiomes of the patients and the control group did not have significant differences in the species richness index (Shannon). However, the patients showed a decrease in the uniformity index, another parameter of alpha diversity. Bacterial community structures (beta diversity) did not differ significantly between patients with localized forms of tuberculosis and healthy subjects. In patients with limited forms of tuberculosis, contrary to the decrease in the content of representatives of the phyla Fusobacteria, TM7, Tenericutes, Spirochaetes, and SR1, and of the genera Dialister, Mycoplasma, and Filifactor in the sputum, no clear dominance of any bacterial taxon was observed. Conclusion. Certain alpha and beta diversity parameters that characterize the sputum microbiome of patients with localized forms of pulmonary tuberculosis need to be confirmed in independent large-scale studies to further understand the role of the sputum microbiota in the development of localized forms of pulmonary tuberculosis. Determination of Prevotella titers in the sputum of these patients holds promise for the diagnosis of localized forms of pulmonary tuberculosis and the search for their genomic markers.

Subsoiling tillage increased core microbiome associated with nitrogen fixation in the fallow season under rainfed maize monoculture

Subsoiling tillage (ST) is a promising agronomy practice to improve soil physicochemical properties, soil microbial diversity during the crop growing season, and ultimately crop yield, but little is known about whether and how the ST practice will impact soil physicochemical properties and microbial communities in fallow season and their impacts on crop growth in next season. Here, a four-year continuous field experiment was conducted to compare the impacts of three tillage treatments, i.e., the ST, the no-tillage (NT), and the rotary tillage (RT), on soil physicochemical properties and microbial communities in maize fallow season. The results showed that compared with the RT treatment, the ST treatment improved maize yield by 2.3%, 4.2%, 11.4%, and 9.7% from 2018 to 2021, respectively, while there was no significant yield loss between the NT and RT. The ST treatment improved root biomass and soil available nitrogen by 25.1% and 34.0%, respectively, but scarcely impacted soil bulk density and water-filled pore space in comparison with the RT treatment in the maize fallow season in 2021. In addition, changes in root biomass further altered soil bacterial core microbiomes. Compared with the RT treatment, the ST treatment increased the relative abundance of core microbiomes related to nitrogen fixation and denitrification by 169.5% and 62.0%, respectively, but reduced the relative abundance of core microbiomes related to nitrification by 39.0%. The potential functional profile of core microbiomes predicted by the FAPROTAX database also showed that the ST treatment significantly improved nitrogen fixation and ureolysis by 115.9% and 346.9%, respectively, while decreased nitrification by 57.1% in comparison with the RT treatment. The results of the structural equation model showed that ST-induced changes in the function of nitrogen fixation improved soil available nitrogen content in the maize fallow season, which could supply nutrients for maize growth in the next growing season. Additionally, although the NT treatment improved microbial diversities in comparison with the RT and ST treatments, it reduced the relative abundance of microbiomes related to nitrogen cycling in the maize fallow season. These results indicate that the subsoiling tillage could increase the abundance of core microbiomes related to nitrogen fixation and mineralization, which increase soil available nitrogen content in the fallow season of maize cropping in the northeast of China.

Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem

Extensive use of chemicals like herbicides in rice and other fields to manage weeds is expected to have a lasting influence on the soil environment. Considering this rationale, we aimed to decipher the effects of herbicides, Pendimethalin and Pretilachlor, applied at 0.5 and 0.6 kg ha−1, respectively on the rhizosphere microbial community and soil characteristics in the tropical rice field, managed under zero tillage cultivation. The quantity of herbicide residues declined gradually since application up to 60 days thereafter it reached the non-detectable level. Most of the soil variables viz., microbial biomass, soil enzymes etc., exhibited slight reduction in the treated soils compared to the control. A gradual decline was observed in Mineral-N, MBC, MBN and enzyme activities. Quantitative polymerase chain reaction results showed maximal microbial abundance of bacteria, fungi and archaea at mid-flowering stage of rice crop. The 16 rRNA and ITS region targeted amplicons high throughput sequencing microbial metagenomic approach revealed total of 94, 1353, and 510 species for archaea, bacteria and fungi, respectively. The metabarcoding of core microbiota revealed that the archaea comprised of Nitrososphaera, Nitrosocosmicus, and Methanosarcina. In the bacterial core microbiome, Neobacillus, Nitrospira, Thaurea, and Microvigra were found as the predominant taxa. Fusarium, Clonostachys, Nigrospora, Mortierella, Chaetomium, etc., were found in core fungal microbiome. Overall, the study exhibited that the recommended dose of herbicides found to be detrimental to the microbial dynamics, though a negative relation between residues and soil variables was observed that might alter the microbial diversity. The outcomes offer a comprehensive understanding of how herbicides affect the microbial community in zero tillage rice soil, thus has a critical imputation for eco-friendly and sustainable rice agriculture. Further, the long-term studies will be helpful in elucidating the role of identified microbial groups in sustaining the soil fertility and crop productivity.

Comparative bacteriome and antibiotic resistome analysis of water and sediment of the Ganga River of India.

A comparative analysis between water and sediment can provide better information to understand the dynamics of the inhabitant microbiome and their respective antibiotic resistance genes of a river. Therefore, the present investigation was carried to explore the limited information available on bacterial microbiome and their predictive antibiotic resistance genes (ARGs) from water and sediment of the Ganga River. The study utilized the NGS-based sequences previously submitted under the accession number (PRJNA847424 and PRJNA892876). Overall analysis revealed that twenty phyla and fifty-four genera were shared between the water and sediment of the Ganga River. Of them, nine phyla and nineteen genera were observed as significantly different (p-value < 0.05). Where the majority of the genera were associated with the sediment samples over the water that identify the sediment samples as more diverse for species richness. Similarly, seventy-six ARGs were shared between water and sediment samples. Of the ten abundant antibiotic resistance pathways, seven were relatively abundant in sediment samples as compared to the water. Vancomycin resistance genes were significantly more abundant among sediment samples, whereas β-lactam resistance genes were equally distributed in water and sediment samples. The network analysis further revealed that five genera (Flavobacterium, Pseudomonas, Acinetobacter, Candidatus_divison CL5003, and Candidatus_division SWB02) showed a significantly positive correlation with six antibiotic resistance pathways (β-lactam, vancomycin, multidrug resistance, tetracycline, aminoglycoside, and macrolide resistance pathways). The study comes out with several findings where sediment may be considered as a more atrocious habitat for evolving the resistance mechanisms against threatful antibiotics over the water samples of the Ganga River.