The prevalence of many chronic diseases has increased over the last decades. It has been postulated that dysbiosis driven by environmental factors such as antibiotic use is shifting the microbiome in ...ways that increase inflammation and the onset of chronic disease. Dysbiosis can be defined through the loss or gain of bacteria that either promote health or disease, respectively. Here we use multiple independent datasets to determine the nature of dysbiosis for a cluster of chronic diseases that includes urinary stone disease (USD), obesity, diabetes, cardiovascular disease, and kidney disease, which often exist as co-morbidities. For all disease states, individuals exhibited a statistically significant association with antibiotics in the last year compared to healthy counterparts. There was also a statistically significant association between antibiotic use and gut microbiota composition. Furthermore, each disease state was associated with a loss of microbial diversity in the gut. Three genera, Bacteroides, Prevotella, and Ruminococcus, were the most common dysbiotic taxa in terms of being enriched or depleted in disease populations and was driven in part by the diversity of operational taxonomic units (OTUs) within these genera. Results of the cross-sectional analysis suggest that antibiotic-driven loss of microbial diversity may increase the risk for chronic disease. However, longitudinal studies are needed to confirm the causative effect of diversity loss for chronic disease risk.
There is a growing appreciation for the importance of the gut microbiota as a therapeutic target in various diseases. However, there are only a handful of known commensal strains that can potentially ...be used to manipulate host physiological functions. Here we isolate a consortium of 11 bacterial strains from healthy human donor faeces that is capable of robustly inducing interferon-γ-producing CD8 T cells in the intestine. These 11 strains act together to mediate the induction without causing inflammation in a manner that is dependent on CD103
dendritic cells and major histocompatibility (MHC) class Ia molecules. Colonization of mice with the 11-strain mixture enhances both host resistance against Listeria monocytogenes infection and the therapeutic efficacy of immune checkpoint inhibitors in syngeneic tumour models. The 11 strains primarily represent rare, low-abundance components of the human microbiome, and thus have great potential as broadly effective biotherapeutics.
Connections between the gut and brain monitor the intestinal tissue and its microbial and dietary content
, regulating both physiological intestinal functions such as nutrient absorption and motility
..., and brain-wired feeding behaviour
. It is therefore plausible that circuits exist to detect gut microorganisms and relay this information to areas of the central nervous system that, in turn, regulate gut physiology
. Here we characterize the influence of the microbiota on enteric-associated neurons by combining gnotobiotic mouse models with transcriptomics, circuit-tracing methods and functional manipulations. We find that the gut microbiome modulates gut-extrinsic sympathetic neurons: microbiota depletion leads to increased expression of the neuronal transcription factor cFos, and colonization of germ-free mice with bacteria that produce short-chain fatty acids suppresses cFos expression in the gut sympathetic ganglia. Chemogenetic manipulations, translational profiling and anterograde tracing identify a subset of distal intestine-projecting vagal neurons that are positioned to have an afferent role in microbiota-mediated modulation of gut sympathetic neurons. Retrograde polysynaptic neuronal tracing from the intestinal wall identifies brainstem sensory nuclei that are activated during microbial depletion, as well as efferent sympathetic premotor glutamatergic neurons that regulate gastrointestinal transit. These results reveal microbiota-dependent control of gut-extrinsic sympathetic activation through a gut-brain circuit.
•In vitro fermentation behavior of P. haitanensis polysaccharides (PHP) was studied.•PHP could significantly alter the composition and diversity of gut microflora.•PHP could significantly promote the ...production of short-chain fatty acids.•Molecular weight and intrinsic viscosity of PHP decreased during fermentation.•Degradation products ranged from DP 2 to 9, with the main linkage patterns being 1 → 3 and 1 → 4 linked Galp.
This study applied an in vitro fermentation model, whereby the catabolism of Porphyra haitanensis polysaccharides (PHP) was monitored coupled with the variations of microbiota composition and the concentration of short-chain fatty acids (SCFAs), so as to assess the effects of PHP on human intestinal microbiota. After 24 h anaerobic incubation, the level of microflora diversity increased significantly, as the microbiome structure was reshaped through promotion of intestinal probiotics proliferation and inhibition of pathogens growth. Besides, the final concentration of total SCFAs increased to 32.32 ± 1.81 mmol/L, and contained high amounts of acetic, propionic and butyric acid. Furthermore, the molecular weight of PHP decreased from 2.623 × 105 g/mol to 2.308 × 104 g/mol. The degree of polymerization of oligosaccharide products ranged from 2 to 9, with the main linkage patterns being 1 → 3 and 1 → 4 linked Galp. The current study provides new insight on the probiotic activity of PHP within the human gastrointestinal tract.
Bacteria have been widely exploited as bioagents for applications in diagnosis and treatment, benefitting from their living characteristics including colonization, rapid proliferation, and facile ...genetic manipulation. As such, bacteria being tailored to perform precisely in the right place at the right time to avoid potential side effects would be of great importance but has proven to be difficult. Here, a strategy of on‐demand bacterial reactivation is described by individually restraining within a triggerable nanocoating. Upon reaching at a location of interest, nanocoatings can be triggered to dissolution in situ and subsequently decoat the bacteria which are able to recover their bioactivities as needed. It is demonstrated that gut microbiota coated with an enteric nanocoating can respond to gastrointestinal environments and reactivate in the intestine by a pH‐triggered decoating. In virtue of this unique, coated bacteria remain inactive following oral administration to exempt acidic insults, while revive to restore therapeutic effects after gastric emptying. Consequently, improved oral availability and treatment efficacy are achieved in two mouse models of intestinal infection. Bacteria restrained by a triggerable nanocoating represent a smart therapeutic that can take effect when necessary. On‐demand bacterial reactivation suggests a robust platform for the development of precision bacterial‐mediated bioagents.
Bacteria being tailored to perform therapeutic effects precisely in the right place at the right time to avoid potential side effects is important but has proven to be challenging. A strategy of on‐demand bacterial reactivation is described by restraining within a triggerable nanocoating. Upon reaching at a location of interest, the bacteria can be liberated to reactivate as needed.
Soil microbial communities directly affect soil functionality through their roles in the cycling of soil nutrients and carbon storage. Microbial communities vary substantially in space and time, ...between soil types and under different land management. The mechanisms that control the spatial distributions of soil microbes are largely unknown as we have not been able to adequately upscale a detailed analysis of the microbiome in a few grams of soil to that of a catchment, region or continent. Here we reveal that soil microbes along a 1000 km transect have unique spatial structures that are governed mainly by soil properties. The soil microbial community assessed using Phospholipid Fatty Acids showed a strong gradient along the latitude gradient across New South Wales, Australia. We found that soil properties contributed the most to the microbial distribution, while other environmental factors (e.g., temperature, elevation) showed lesser impact. Agricultural activities reduced the variation of the microbial communities, however, its influence was local and much less than the overall influence of soil properties. The ability to predict the soil and environmental factors that control microbial distribution will allow us to predict how future soil and environmental change will affect the spatial distribution of microbes.
The dense microbial ecosystem in the gut is intimately connected to numerous facets of human biology, and manipulation of the gut microbiota has broad implications for human health. In the absence of ...profound perturbation, the bacterial strains that reside within an individual are mostly stable over time
. By contrast, the fate of exogenous commensal and probiotic strains applied to an established microbiota is variable, generally unpredictable and greatly influenced by the background microbiota
. Therefore, analysis of the factors that govern strain engraftment and abundance is of critical importance to the emerging field of microbiome reprogramming. Here we generate an exclusive metabolic niche in mice via administration of a marine polysaccharide, porphyran, and an exogenous Bacteroides strain harbouring a rare gene cluster for porphyran utilization. Privileged nutrient access enables reliable engraftment of the exogenous strain at predictable abundances in mice harbouring diverse communities of gut microbes. This targeted dietary support is sufficient to overcome priority exclusion by an isogenic strain
, and enables strain replacement. We demonstrate transfer of the 60-kb porphyran utilization locus into a naive strain of Bacteroides, and show finely tuned control of strain abundance in the mouse gut across multiple orders of magnitude by varying porphyran dosage. Finally, we show that this system enables the introduction of a new strain into the colonic crypt ecosystem. These data highlight the influence of nutrient availability in shaping microbiota membership, expand the ability to perform a broad spectrum of investigations in the context of a complex microbiota, and have implications for cell-based therapeutic strategies in the gut.
The impact of maternal microbial influences on the early choreography of the neonatal calf microbiome were investigated. Luminal content and mucosal scraping samples were collected from ten locations ...in the calf gastrointestinal tract (GIT) over the first 21 days of life, along with postpartum maternal colostrum, udder skin, and vaginal scrapings. Microbiota were found to vary by anatomical location, between the lumen and mucosa at each GIT location, and differentially enriched for maternal vaginal, skin, and colostral microbiota. Most calf sample sites exhibited a gradual increase in α-diversity over the 21 days beginning the first few days after birth. The relative abundance of Firmicutes was greater in the proximal GIT, while Bacteroidetes were greater in the distal GIT. Proteobacteria exhibited greater relative abundances in mucosal scrapings relative to luminal content. Forty-six percent of calf luminal microbes and 41% of mucosal microbes were observed in at-least one maternal source, with the majority being shared with microbes on the skin of the udder. The vaginal microbiota were found to harbor and uniquely share many common and well-described fibrolytic rumen bacteria, as well as methanogenic archaea, potentially indicating a role for the vagina in populating the developing rumen and reticulum with microbes important to the nutrition of the adult animal.
The diversity and basic functional attributes of the gut microbiome of healthy Indians is not well understood. This study investigated the gut microbiome of three Indian communities: individuals ...residing in rural and urban (n = 49) sea level Ballabhgarh areas and in rural high altitude areas of Leh, Ladakh in North India (n = 35). Our study revealed that the gut microbiome of Indian communities is dominated by Firmicutes followed by Bacteroidetes, Actinobateria and Proteobacteria. Although, 54 core bacterial genera were detected across the three distinct communities, the gut bacterial composition displayed specific signatures and was observed to be influenced by the topographical location and dietary intake of the individuals. The gut microbiome of individuals living in Leh was observed to be significantly similar with a high representation of Bacteroidetes and low abundance of Proteobacteria. In contrast, the gut microbiome of individuals living in Ballabhgarh areas harbored higher number of Firmicutes and Proteobacteria and is enriched with microbial xenobiotic degradation pathways. The rural community residing in sea level Ballabhgarh areas has unique microbiome characterized not only by a higher diversity, but also a higher degree of interindividual homogeneity.
Plasma agriculture details the role of nonthermal plasma in the development of plants from seeds to crops. Several publications reported enhanced plant growth, improved stress tolerance, and ...antimicrobial effects of plasma treatment and plasma‐treated water. In this review, we present an overview of the recent plasma agriculture literature and put it in the context of the plant needs and the effects on the plant ecosystem. We will discuss key developmental stages of plants and their needs, the different growth environments from hydroponics to soilless and soil substrates, and the plant microbiome. This review provides the context to design plasma‐based fertilization strategies to address the needs of plants and their ecosystem.
Plasma agriculture is beneficial for plant development from the seed to the crop level. This review describes the different growth stages, the plant's needs in each development stage, and the role of plasma treatment. The role of the plant environment is discussed. Recent plasma agriculture literature is put in the context with the plant and its ecosystem's needs in focus.
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