Plastics waste and microplastics including polyethylene (PE) and polystyrene (PS) have been an environmental concern for years. Recent research has revealed that larvae of Galleria mellonella are ...capable of biodegrading low density PE film. In this study, we tested the feasibility of enhancing larval survival and the effect of supplementing the co-diet on plastic degradation by feeding the larvae beeswax or wheat bran as a co-diet. Significant mass loss of plastic was observed over a 21-day period, i.e., with respective consumption of 0.88 and 1.95 g by 150 larvae fed only either PS or PE. The formation of CO and C–O containing functional groups and long chain fatty acids as the metabolic intermediates of plastics in the residual polymers indicated depolymerization and biodegradation. Supplementing beeswax and bran increased the survival rates but decreased the consumption of plastic. The changes in the gut microbiome revealed that Bacillus and Serratia were significantly associated with the PS and PE diets. Beeswax and bran showed different shaping effects on the core gut microbiome of larvae fed the PE and PS. These results suggest that supplementing the co-diet affected the physiological properties of the larvae and plastic biodegradation and shaped the core gut microbiome.
Gut microbiota affects health, metabolism and immunity of the host, and in the case of livestock, also food-safety. Here, 16S rRNA gene high-throughput Illumina sequencing was used to describe the ...microbiome of chicken caeca in two different breeds and management systems throughout their whole productive lifespan. Broilers (Ross-308), as a fast-growing breed reared in an intensive system for 42-days, and a slow-growing breed of chicken (Sasso-T451A) reared in an extensive farming system with outdoor access for 86-days, were compared. The core microbiome and differentially abundant taxa, as well as taxa associated with age were identified. Age was identified as the strongest influencing factor in caecal microbiota composition, and, in general, each age-group showed an age-associated community profile, with a transition period at the middle of their lifespan. However, substantial differences were observed in the composition of caecal microbiota of both chicken breeds, microbiota being richer and more complex in free-range chicken than in broilers. Several taxa positively/negatively correlated with Campylobacter relative abundance were also identified. Especially noteworthy was the identification by microbial community comparison of microbiota profiles suggestive of dysbiosis in several free-range chickens, probably associated to the typhlitis observed in the lumen of their caeca.
A mosaic of cross-phylum chemical interactions occurs between all metazoans and their microbiomes. A number of molecular families that are known to be produced by the microbiome have a marked effect ...on the balance between health and disease
. Considering the diversity of the human microbiome (which numbers over 40,000 operational taxonomic units
), the effect of the microbiome on the chemistry of an entire animal remains underexplored. Here we use mass spectrometry informatics and data visualization approaches
to provide an assessment of the effects of the microbiome on the chemistry of an entire mammal by comparing metabolomics data from germ-free and specific-pathogen-free mice. We found that the microbiota affects the chemistry of all organs. This included the amino acid conjugations of host bile acids that were used to produce phenylalanocholic acid, tyrosocholic acid and leucocholic acid, which have not previously been characterized despite extensive research on bile-acid chemistry
. These bile-acid conjugates were also found in humans, and were enriched in patients with inflammatory bowel disease or cystic fibrosis. These compounds agonized the farnesoid X receptor in vitro, and mice gavaged with the compounds showed reduced expression of bile-acid synthesis genes in vivo. Further studies are required to confirm whether these compounds have a physiological role in the host, and whether they contribute to gut diseases that are associated with microbiome dysbiosis.
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.
Symbioses between insects and microbes are ubiquitous, but vary greatly in terms of function, transmission mechanism, and location in the insect. Lepidoptera (butterflies and moths) are one of the ...largest and most economically important insect orders; yet, in many cases, the ecology and functions of their gut microbiomes are unresolved. We used high-throughput sequencing to determine factors that influence gut microbiomes of field-collected fall armyworm (Spodoptera frugiperda) and corn earworm (Helicoverpa zea). Fall armyworm midgut bacterial communities differed from those of corn earworm collected from the same host plant species at the same site. However, corn earworm bacterial communities differed between collection sites. Subsequent experiments using fall armyworm evaluating the influence of egg source and diet indicated that that host plant had a greater impact on gut communities. We also observed differences between regurgitant (foregut) and midgut bacterial communities of the same insect host, suggesting differential colonization. Our findings indicate that host plant is a major driver shaping gut microbiota, but differences in insect physiology, gut region, and local factors can also contribute to variation in microbiomes. Additional studies are needed to assess the mechanisms that affect variation in insect microbiomes, as well as the ecological implications of this variability in caterpillars.
Potentially beneficial microorganisms have been inoculated into agricultural soils for years. However, concurrent with sequencing advances and successful manipulation of host-associated microbiomes, ...industry and academia have recently boosted investments into microbial inoculants, convinced they can increase crop yield and reduce fertilizer and pesticide requirements. The efficacy of soil microbial inoculants remains unreliable, and unlike crop breeding, in which target traits (e.g., yield) have long been considered alongside environmental compatibility, microbial inoculant ecology is not sufficiently integrated into microbial selection and production. We propose a holistic temporal model of the shifting constraints on inoculants at five stages of product development and application, and highlight potential conflicts between stages. We question the feasibility of developing ideal soil microbial inoculants with current approaches.
Certain soil microorganisms can perform agriculturally valuable functions such as ethylene reduction, plant pathogen suppression, and soil nutrient solubilization.
Interest and investment in developing soil microbial inoculants to enhance these functions has recently surged, but in-field product success remains unpredictable and unreliable.
Microbial inoculants tend to be chosen based on their activity in controlled laboratory screenings and for ease of mass cultivation, with minimal regard for ecologically relevant traits that will both allow them to survive in the field during a target functional period and prevent excessive persistence.
We highlight the conflicting roles of microbial inoculant traits at each product stage, and how this may complicate selection for microorganisms that function as desired in the field.
The gut microbiota of preterm infants develops predictably
, with pioneer species colonizing the gut after birth, followed by an ordered succession of microorganisms. The gut microbiota is vital to ...the health of preterm infants
, but the forces that shape these predictable dynamics of microbiome assembly are unknown. The environment, the host and interactions between microorganisms all potentially shape the dynamics of the microbiota, but in such a complex ecosystem, identifying the specific role of any individual factor is challenging
. Here we use multi-kingdom absolute abundance quantification, ecological modelling and experimental validation to address this challenge. We quantify the absolute dynamics of bacteria, fungi and archaea in a longitudinal cohort of 178 preterm infants. We uncover microbial blooms and extinctions, and show that there is an inverse correlation between bacterial and fungal loads in the infant gut. We infer computationally and demonstrate experimentally in vitro and in vivo that predictable assembly dynamics may be driven by directed, context-dependent interactions between specific microorganisms. Mirroring the dynamics of macroscopic ecosystems
, a late-arriving member of the microbiome, Klebsiella, exploits the pioneer microorganism, Staphylococcus, to gain a foothold within the gut. Notably, we find that interactions between different kingdoms can influence assembly, with a single fungal species-Candida albicans-inhibiting multiple dominant genera of gut bacteria. Our work reveals the centrality of simple microbe-microbe interactions in shaping host-associated microbiota, which is critical both for our understanding of microbiota ecology and for targeted microbiota interventions.
Differences in the presence of even a few genes between otherwise identical bacterial strains may result in critical phenotypic differences. Here we systematically identify microbial genomic ...structural variants (SVs) and find them to be prevalent in the human gut microbiome across phyla and to replicate in different cohorts. SVs are enriched for CRISPR-associated and antibiotic-producing functions and depleted from housekeeping genes, suggesting that they have a role in microbial adaptation. We find multiple associations between SVs and host disease risk factors, many of which replicate in an independent cohort. Exploring genes that are clustered in the same SV, we uncover several possible mechanistic links between the microbiome and its host, including a region in Anaerostipes hadrus that encodes a composite inositol catabolism-butyrate biosynthesis pathway, the presence of which is associated with lower host metabolic disease risk. Overall, our results uncover a nascent layer of variability in the microbiome that is associated with microbial adaptation and host health.
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.
The gut microbiota synthesize hundreds of molecules, many of which influence host physiology. Among the most abundant metabolites are the secondary bile acids deoxycholic acid (DCA) and lithocholic ...acid (LCA), which accumulate at concentrations of around 500 μM and are known to block the growth of Clostridium difficile
, promote hepatocellular carcinoma
and modulate host metabolism via the G-protein-coupled receptor TGR5 (ref.
). More broadly, DCA, LCA and their derivatives are major components of the recirculating pool of bile acids
; the size and composition of this pool are a target of therapies for primary biliary cholangitis and nonalcoholic steatohepatitis. Nonetheless, despite the clear impact of DCA and LCA on host physiology, an incomplete knowledge of their biosynthetic genes and a lack of genetic tools to enable modification of their native microbial producers limit our ability to modulate secondary bile acid levels in the host. Here we complete the pathway to DCA and LCA by assigning and characterizing enzymes for each of the steps in its reductive arm, revealing a strategy in which the A-B rings of the steroid core are transiently converted into an electron acceptor for two reductive steps carried out by Fe-S flavoenzymes. Using anaerobic in vitro reconstitution, we establish that a set of six enzymes is necessary and sufficient for the eight-step conversion of cholic acid to DCA. We then engineer the pathway into Clostridium sporogenes, conferring production of DCA and LCA on a nonproducing commensal and demonstrating that a microbiome-derived pathway can be expressed and controlled heterologously. These data establish a complete pathway to two central components of the bile acid pool.
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