Members Of Bacteroidetes Research Articles

Short-term effect of no-tillage management on the chemical attributes and bacterial diversity in soils in an organic production system

No-tillage (NT) has been adopted in organic agriculture as an alternative to conventional tillage (CT) for improving soil conservation. Cover crops (CC) play a vital role in this process by providing straw and releasing nutrients into the soil. Therefore, in this study, we aimed to evaluate the effects of NT and CT management on the chemical properties and bacterial diversity of soil following the cultivation of diverse CC in an organic system. The experiment was conducted using a randomized block design with subdivided plots, wherein the plots represented CT and NT, and the subplots represented the diverse CC tested, including pearl millet, sunn hemp, jack bean, seed mixes 1 and 2 (containing 100 % and 50 % of the recommended seeding rates for each crop), and spontaneous plants. The evaluations were conducted one year after the experiment was conducted. The results demonstrated that NT promoted increases in soil magnesium, phosphorus, and organic carbon contents, including increased bacterial richness. Moreover, NT resulted in a higher abundance of Bacteroidetes, GAL15, and Myxococcota. Conversely, CT favored a greater relative abundance of Actinobacteria, in addition to the members of Bacteroidetes. Regarding the influence of CC, no significant differences were observed in the diversity and structure of the bacterial communities, except for subgroup 17, which was more abundant in spontaneously grown plants. NT proved to be more effective than CT in improving soil chemical properties and bacterial diversity, implying its potential to contribute to sustainable agricultural systems.

Lactobacillus delbrueckii CIDCA 133 fermented milk modulates inflammation and gut microbiota to alleviate acute colitis

Lactobacillus delbrueckii subsp. lactis CIDCA 133 is a health-promoting bacterium that can alleviate gut inflammation and improve the epithelial barrier in a mouse model of mucositis. Despite these beneficial effects, the protective potential of this strain in other inflammation models, such as inflammatory bowel disease, remains unexplored. Herein, we examined for the first time the efficacy of Lactobacillus delbrueckii CIDCA 133 incorporated into a fermented milk formulation in the recovery of inflammation, epithelial damage, and restoration of gut microbiota in mice with dextran sulfate sodium-induced colitis. Oral administration of Lactobacillus delbrueckii CIDCA 133 fermented milk relieved colitis by decreasing levels of inflammatory factors (myeloperoxidase, N-acetyl-β-D-glucosaminidase, toll-like receptor 2, nuclear factor-κB, interleukins 10 and 6, and tumor necrosis factor), secretory immunoglobulin A levels, and intestinal paracellular permeability. This immunobiotic also modulated the expression of tight junction proteins (zonulin and occludin) and the activation of short-chain fatty acids-related receptors (G-protein coupled receptors 43 and 109A). Colonic protection was effectively associated with acetate production and restoration of gut microbiota composition. Treatment with Lactobacillus delbrueckii CIDCA 133 fermented milk increased the abundance of Firmicutes members (Lactobacillus genus) while decreasing the abundance of Proteobacteria (Helicobacter genus) and Bacteroidetes members (Bacteroides genus). These promising outcomes influenced the mice’s mucosal healing, colon length, body weight, and disease activity index, demonstrating that this immunobiotic could be explored as an alternative approach for managing inflammatory bowel disease.

Firmicutes and Bacteroidetes contribute to mass gain variation in female obligate hibernators

Abstract Obtaining body condition is an important life history challenge that directly impacts individual fitness and is particularly important for hibernating animals, whose maintenance of adequate body fat and mass is essential for survival. It is well-documented that host-associated microorganisms play a vital role in animal physiology and behavior. Recent work demonstrates that gut microbes are associated with fat accumulation and obesity, particularly the phyla Firmicutes and Bacteroidetes. The focus of most microbiome studies has been on human health or involved lab-reared animals used as a model system. However, these microbes likely are important for individual fitness in wild populations and provide potential mechanistic insights into the adaptability and survival of wildlife. Here we tested whether symbiotic microorganisms within the phyla of Firmicutes and Bacteroidetes were associated with summer mass gain in an exceptionally well-studied wild population of yellow-bellied marmots (Marmota flaviventer) by analyzing 207 fecal samples collected over 5 summer active seasons. Results showed that marmots with higher mass gain rates had a greater relative abundance of Firmicutes. In contrast, a higher relative abundance of Bacteroidetes was associated with lower mass gain rates, but only for marmots living in harsher environments. Similar patterns were found at the family level where Ruminococcaceae, a member of Firmicutes, was associated with higher mass gain rates, and Muribaculaceae, a member of Bacteroidetes, was associated with lower mass gain rates in harsher environments. Although correlative, these results highlight the potential importance of symbiotic gut microbiota to mass gain in the wild—a trait associated with survival and fitness in many taxonomic groups.

Aridification alters the diversity of airborne bacteria in drylands of China

Dryland ecosystems, which vary sensitively to drought owing to climate change and human activities, frequently cause large-scale aeolian dispersal of terrestrial-mineral and biological particles. To date, very few studies have focused on the atmosphere-land exchange of bacteria in drylands. To understand the bacterial transport from the terrestrial environment to the atmosphere over drylands, soil and aerosol samples were collected at 19 sites in arid and semi-arid regions across drylands of China in the summer of 2017. The 16S rRNA gene sequencing revealed that the bacterial diversity in the atmosphere was significantly lower than that in terrestrial ecosystems for all the collected samples. Moreover, bacterial diversity in the atmosphere increases in arid regions compared to semi-arid regions, while those of the terrestrial environment were maintained regardless of the region. Additionally, the terrestrial bacterial sources contributed to the airborne bacteria more significantly in arid regions than those in semi-arid regions (accounting for 10.0 ± 1.1% and 3.5 ± 1.1%, respectively). The arid conditions tended to enhance the atmospheric emissions of Chloroflexi, while the members of Bacteroidetes were dominant in both the atmospheres of the semi-arid and arid regions. The differences in bacterial community structures between the terrestrial and atmospheric ecosystems are thought to depend on the ground surface characteristics such as vegetation and terrestrial substrates. Meteorological drought may alter terrestrial characteristics, which regulate airborne bacterial dispersal from dryland to its downwind regions, suggesting that more attention should be paid to the bacterial roles in the biology-health-climate process in the future.

Dynamics and ecological reassembly of the human gut microbiome and the host metabolome in response to prolonged fasting.

Prolonged fasting is an intervention approach with potential benefits for individuals with obesity or metabolic disorders. Changes in gut microbiota during and after fasting may also have significant effects on the human body. Here we conducted a 7-days medically supervised water-only fasting for 46 obese volunteers and characterized their gut microbiota based on whole-metagenome sequencing of feces at five timepoints. Substantial changes in the gut microbial diversity and composition were observed during fasting, with rapid restoration after fasting. The ecological pattern of the microbiota was also reassembled during fasting, reflecting the reduced metabolic capacity of diet-derived carbohydrates, while other metabolic abilities such as degradation of glycoproteins, amino acids, lipids, and organic acid metabolism, were enhanced. We identified a group of species that responded significantly to fasting, including 130 fasting-resistant (consisting of a variety of members of Bacteroidetes, Proteobacteria, and Fusobacteria) and 140 fasting-sensitive bacteria (mainly consisting of Firmicutes members). Functional comparison of the fasting-responded bacteria untangled the associations of taxon-specific functions (e.g., pentose phosphate pathway modules, glycosaminoglycan degradation, and folate biosynthesis) with fasting. Furthermore, we found that the serum and urine metabolomes of individuals were also substantially changed across the fasting procedure, and particularly, these changes were largely affected by the fasting-responded bacteria in the gut microbiota. Overall, our findings delineated the patterns of gut microbiota alterations under prolonged fasting, which will boost future mechanistic and clinical intervention studies.

Intravenous ferric carboxymaltose and ferric derisomaltose alter the intestinal microbiome in female iron-deficient anemic mice.

Iron deficiency anemia (IDA) is a leading global health concern affecting approximately 30% of the population. Treatment for IDA consists of replenishment of iron stores, either by oral or intravenous (IV) supplementation. There is a complex bidirectional interplay between the gut microbiota, the host's iron status, and dietary iron availability. Dietary iron deficiency and supplementation can influence the gut microbiome; however, the effect of IV iron on the gut microbiome is unknown. We studied how commonly used IV iron preparations, ferric carboxymaltose (FCM) and ferric derisomaltose (FDI), affected the gut microbiome in female iron-deficient anemic mice. At the phylum level, vehicle-treated mice showed an expansion in Verrucomicrobia, mostly because of the increased abundance of Akkermansia muciniphila, along with contraction in Firmicutes, resulting in a lower Firmicutes/Bacteroidetes ratio (indicator of dysbiosis). Treatment with either FCM or FDI restored the microbiome such that Firmicutes and Bacteroidetes were the dominant phyla. Interestingly, the phyla Proteobacteria and several members of Bacteroidetes (e.g., Alistipes) were expanded in mice treated with FCM compared with those treated with FDI. In contrast, several Clostridia class members were expanded in mice treated with FDI compared with FCM (e.g., Dorea spp., Eubacterium). Our data demonstrate that IV iron increases gut microbiome diversity independently of the iron preparation used; however, differences exist between FCM and FDI treatments. In conclusion, replenishing iron stores with IV iron preparations in clinical conditions, such as inflammatory bowel disease or chronic kidney disease, could affect gut microbiome composition and consequently contribute to an altered disease outcome.

Bacterial composition and antibiotic resistome profile of water in the Manila Bay South Harbor

Anthropogenic activities in Manila Bay, the oldest and busiest international port in the Philippines, may cause changes in flora and fauna within its harbors. Specifically, the ballasting and deballasting of ships may accidentally introduce new populations of microorganisms, plants, and animals. Ballasting (and deballasting), or the process of carrying in/out of seawater from ship tanks in major ports/harbors, are causing major disturbances, particularly in marine ecosystems. Previous studies have shown that marine microorganisms comprise 98% of the primary production and regulation of the ocean's biogeochemical processes. However, with the continuous community disturbances due to human influence, potential marine bacterial populations with antibiotic resistomes may occur, and impact marine diversity. Since data on the microbial communities in Manila Bay South Harbor are limited, this study determined the bacterial composition and antibiotic resistome profiles of water samples from the area. Next-generation sequencing techniques and culture-based methods were utilized to elucidate the bacterial and functional diversity, as well as the antibiotic resistome of the water samples from the Manila Bay South Harbor. The bacterial diversity of the water sample was made up primarily of members of Bacteroidetes, Firmicutes, and Prevotella. The Clusters of Orthologous Group (COG) Level 1 identified metabolism as the most dominant functional predicted metagenome. The characterization of antibiotic resistance genes (ARGs) from water samples revealed that ARGs encoding resistance to multidrug was the most abundant. On the other hand, the identified antibiotic-resistant bacteria included ampicillin-resistant Escherichia coli, multidrug-resistant Klebsiella pneumoniae, ampicillin- and cefuroxime-resistant Vibrio alginolyticus and ampicillin resistant Vibrio furnissii. The above results provide a baseline marine bacterial community and antibiotic resistome profile of the Manila Bay South Harbor. This information is critical in gaining a better understanding of the potential roles of shifts in marine microbiomes, and in turn, help in developing appropriate solutions for managing the undesirable consequences of ballast water.

Bacteroides fragilis expresses three proteins similar to Porphyromonas gingivalis HmuY: Hemophore-like proteins differentially evolved to participate in heme acquisition in oral and gut microbiomes.

Oral and gut microbiomes are important for the maintenance of homeostasis in the human body. Altered or disturbed mutualism between their members results in dysbiosis with local injury and subsequent systemic diseases. The high bacterial density causes intense competition among microbiome residents to acquire nutrients, including iron and heme, the latter of high importance for heme auxotrophic members of the Bacteroidetes phylum. Our main hypothesis is that the heme acquisition mechanism, with the leading role played by a novel HmuY family of hemophore-like proteins, can be used to fulfill nutritional requirements and increase virulence. We characterized HmuY homologs expressed by Bacteroides fragilis and compared their properties with the first representative of this family, the HmuY protein of Porphyromonas gingivalis. In contrast to other Bacteroidetes members, B. fragilis produces three HmuY homologs (Bfr proteins). All bfr transcripts were produced at higher levels in bacteria starved of iron and heme (fold change increase ~60, ~90, and ~70 for bfrA, bfrB, and bfrC, respectively). X-ray protein crystallography showed that B. fragilis Bfr proteins are structurally similar to P. gingivalis HmuY and to other homologs, except for differences in the potential heme-binding pockets. BfrA binds heme, mesoheme, and deuteroheme, but preferentially under reducing conditions, using Met175 and Met146 to coordinate heme iron. BfrB binds iron-free protoporphyrin IX and coproporphyrin III, whereas BfrC does not bind porphyrins. HmuY is capable of heme sequestration from BfrA, which might increase the ability of P. gingivalis to cause dysbiosis also in the gut microbiome.

Neutral and Pectic Heteropolysaccharides Isolated from Opuntia joconostle Mucilage: Composition, Molecular Dimensions and Prebiotic Potential.

Opuntia joconostle is a semi-wild cactus cultivated for its fruit. However, the cladodes are often discarded, wasting the potentially useful mucilage in them. The mucilage is composed primarily of heteropolysaccharides, characterized by their molar mass distribution, monosaccharide composition, structural features (by vibrational spectroscopy, FT IR, and atomic force microscopy, AFM), and fermentability by known saccharolytic commensal members of the gut microbiota. After fractionation with ion exchange chromatography, four polysaccharides were found: one neutral (composed mainly of galactose, arabinose, and xylose) and three acidic, with a galacturonic acid content from 10 to 35%mol. Their average molar masses ranged from 1.8 × 105 to 2.8 × 105 g·mol-1. Distinct structural features such as galactan, arabinan, xylan, and galacturonan motifs were present in the FT IR spectra. The intra- and intermolecular interactions of the polysaccharides, and their effect on the aggregation behavior, were shown by AFM. The composition and structural features of these polysaccharides were reflected in their prebiotic potential. Lactobacilli and Bifidobacteria were not able to utilize them, whereas members of Bacteroidetes showed utilization capacity. The obtained data suggest a high economic potential for this Opuntia species, with potential uses such as animal feed in arid areas, precise prebiotic, and symbiotic formulations, or as the carbon skeleton source in a green refinery. Our methodology can be used to evaluate the saccharides as the phenotype of interest, helping to guide the breeding strategy.

Long-term organic fertilization promotes the resilience of soil multifunctionality driven by bacterial communities

Long-term intensive fertilization is a practice common around the world and gradually alters soil microbiome, however, its influences on the temporal resilience of soil multifunctionality to biodiversity loss and biodiversity-multifunctionality relationships remain poorly understood. Here, we manipulated soil biodiversity using the dilution-to-extinction approach to examine the temporal variability in individual functions, soil multifunctionality and their relationships with bacterial and fungal communities under different fertilization treatments during a 90-day re-colonization process. We found that organic fertilization accelerated the resilience of single functions and soil multifunctionality to biodiversity loss compared with mineral fertilization and unfertilized control. The fungal community was less resilient than bacterial community to disturbances caused by fertilization and dilution. Bacterial but not fungal diversity was significantly and positively related to multifunctionality, and the strength of the diversity-multifunctionality relationships in organic fertilized soil was 3- and 67-fold higher than that in unfertilized and mineral fertilized soil, respectively. Both organic and mineral nutrient inputs promoted copiotroph-dominated bacterial assemblages (including Proteobacteria and Bacteroidetes members) and suppressed oligotrophs (mostly Acidobacteria and Chloroflexi), which paralleled multifunctionality resilience patterns in fertilized soils. β-Diversity of bacterial copiotrophs alone or in combination was significantly related to changes in multifunctionality. Random forest analysis and structural equation modeling indicated that bacterial community diversity and composition along with soil carbon and nitrogen basically determined soil multifunctionality, with 70% of the variance in multifunctionality being explained. Rare taxa from the bacterial copiotrophs were particularly important for maintaining multifunctionality. Our results underline the importance of fertilization-induced shifts in microbial ecophysiological strategies for promoting the resilience of soil multifunctionality to biodiversity loss, and the need to preserve the diversity of rare copiotrophic taxa for stable provision of ecosystem functions under future environmental change.

Limited carbon cycling due to high-pressure effects on the deep-sea microbiome

Deep-sea microbial communities are exposed to high-pressure conditions, which has a variable impact on prokaryotes depending on whether they are piezophilic (that is, pressure-loving), piezotolerant or piezosensitive. While it has been suggested that elevated pressures lead to higher community-level metabolic rates, the response of these deep-sea microbial communities to the high-pressure conditions of the deep sea is poorly understood. Based on microbial activity measurements in the major oceanic basins using an in situ microbial incubator, we show that the bulk heterotrophic activity of prokaryotic communities becomes increasingly inhibited at higher hydrostatic pressure. At 4,000 m depth, the bulk heterotrophic prokaryotic activity under in situ hydrostatic pressure was about one-third of that measured in the same community at atmospheric pressure conditions. In the bathypelagic zone—between 1,000 and 4,000 m depth—~85% of the prokaryotic community was piezotolerant and ~5% of the prokaryotic community was piezophilic. Despite piezosensitive-like prokaryotes comprising only ~10% (mainly members of Bacteroidetes, Alteromonas) of the deep-sea prokaryotic community, the more than 100-fold metabolic activity increase of these piezosensitive prokaryotes upon depressurization leads to high apparent bulk metabolic activity. Overall, the heterotrophic prokaryotic activity in the deep sea is likely to be substantially lower than hitherto assumed, with major impacts on the oceanic carbon cycling.

Activated sludge microbial communities and hydrolytic potential in a full-scale SBR system treating landfill leachate

Landfill leachate, due to its recalcitrant nature and toxicity, poses a serious environmental threat, which requires the implementation of effective treatment processes. In this work, a full-scale treatment system consisting of two Sequencing Batch Reactors (SBRs) was used for the processing of landfill leachate of intermediate to mature age (BOD/COD ratio of 0.16). Biosystem operation resulted in BOD5, COD and TKN removal efficiencies of 81%, 39% and 76%, respectively, whereas the low residual NO3 --N concentration in the effluent (4.01 ± 0.10 mg/L) was indicative of the efficient denitrification process. Assessment of hydrolytic potential of activated sludge revealed high endocellular and extracellular lipase activities, which reached values up to 206 and 141 U/g protein respectively, possibly as the consequence of plastics degradation during maturation process. Implementation of Illumina sequencing indicated the predominance of Alphaproteobacteria, accompanied by members of Bacteroidetes, Betaproteobacteria and Chloroflexi. Paracoccus was the predominant genus identified, followed by representatives of the genera Bellilinea, Flavobacterium, Thauera and Truepera. Nitrosomonas was the major ammonia-oxidizing bacterium (AOB), while nitrite oxidation was mainly achieved by the uncultured nitrite-oxidizing bacterium (NOB) Candidatus Nitrotoga.

Diversity of Free-Living and Particle-Attached Prokaryotes in a River-Influenced Coastal Area of the Northern Adriatic Sea

The Northern Adriatic Sea is a key area of the Mediterranean Sea, strongly affected by freshwater inputs, mainly from the Po River, which bring high amounts of nutrients as well as organic and inorganic particles. Free-living and particle-attached prokaryotes were characterized by 16S rRNA gene amplicon sequencing of size-fractionated samples collected during a diatom bloom in this area. The diversity of free-living and particle-attached prokaryotic assemblages was investigated with the aim to understand how the microbial communities are structured in the two fractions and whether specific microbial groups are associated to one lifestyle or the other. The results highlight a diverse prokaryotic community dominated by Proteobacteria, Bacteroidetes, and, remarkably, Firmicutes. Taxa within Firmicutes and Alphaproteobacteria are identified as the main particle-attached indicators by LEfSe, while members of Bacteroidetes and Gammaproteobacteria were representative of the free-living lifestyle, although they were also usually found as particle-attached. Collectively, the results suggest that both the free-living and the particle-attached lifestyles are a complex combination of specialization and adaptation to local conditions.

Bacteroidetes and Firmicutes Drive Differing Microbial Diversity and Community Composition Among Micro-Environments in the Bovine Rumen.

Ruminants are a critical human food source and have been implicated as a potentially important source of global methane emissions. Because of their unique digestive physiology, ruminants rely upon a symbiotic relationship with the complex and rich community of microorganism in the foregut to allow digestion of complex carbohydrates. This study used 16S rRNA gene sequencing to investigate the composition of microbial communities from three rumen micro-environments of cattle fed identical diets: (1) free fluid, (2) the fibrous pack, and (3) the mucosa. Community composition analysis revealed that while a phylogenetic core including the most abundant and most common ruminal taxa (members of Bacteroidetes and Firmicutes) existed across micro-environments, the abundances of these taxa differed significantly between fluid- and mucosa-associated communities, and specific lineages were discriminant of individual micro-environments. Members of Firmicutes, specifically Clostridiales, Lachnospiraceae, Mogibacteriaceae, Christenellaceae, and Erysipelotrichaceae were significantly more abundant in fluid communities, while members of Bacteroidetes, namely Muribaculaceae and Prevotellaceae were more abundant in mucosa-associated communities. Additionally, Methanobacteriaceae, a family of methanogenic Archaea, was more abundant in fluid-associated communities. A set of four more diverse lineages were discriminant of pack-associated communities that included Succinivibrionaceae, RFP12 (Verruco-5), Fibrobacteraceae, and Spirochaetaceae. Our findings indicate that different ecological niches within each micro-environment have resulted in significant differences in the diversity and community structure of microbial communities from rumen fluid, pack, and mucosa without the influence of diet that will help contextualize the influence of other environmental factors.

Not All Liver Abscesses Are Created Equal: The Impact of Tylosin and Antibiotic Alternatives on Bovine Liver Abscess Microbial Communities and a First Look at Bacteroidetes-Dominated Communities.

Liver abscesses (LAs) are extremely prevalent in cattle and result in significant economic losses due to liver condemnation, decreased growth and production, and lower carcass quality. LAs are commonly attributed to the transition to diets high in rapidly fermentable starch which results in rumen epithelial inflammation that allows pathogenic bacteria to gain entry to liver through transport via the hepatic portal vein. The most common intervention for LAs is the inclusion of antibiotics in feedlot diets, under the supervision of a veterinarian; this treatment is associated with reduced occurrence of LAs in this and other studies. Here, through the largest LA 16S rRNA gene sequencing study to date, we demonstrate that the inclusion of tylosin and antibiotic alternatives (the essential oil limonene and Saccharomyces cerevisiae fermentation product) had little impact on LA microbial community composition. Importantly, members of Bacteroidetes (Bacteroides spp. and Porphyromonas spp.) were identified as the dominant taxa in conjunction with low proportions of Fusobacteria in nearly a quarter (61/259) of all LA communities analyzed in this study. The relative abundances of the phyla Fusobacteria and Bacteroidetes had a strongly negative correlation, and LA microbial communities rarely contained high abundances of both of these dominant phyla. Further, based on the presence of taxa discriminant of Bacteroidetes-dominated LAs within over 400 bovine gut communities, we provide evidence suggestive of Bacteroidetes-dominated abscess communities originating in more distal portions of the bovine gut. Together, these findings suggest that some LA microbial communities may originate from portions of the gut other than the rumen.

Fabrication of astaxanthin-enriched colon-targeted alginate microspheres and its beneficial effect on dextran sulfate sodium-induced ulcerative colitis in mice.

Astaxanthin (Ax) with a strong antioxidant activity is beneficial to human health, but its application is limited by its highly unsaturated structure and poor water-solubility. Ax-enriched colon targeted alginate particles (Ax-Alg) was prepared by high-pressure spraying and ionic gelation, and most of particles was in the range of 0.5-3.2μm in a diameter. The in vitro models showed that Ax-Alg can maintain the structural integrity in the different conditions (pH, heat and ion). In addition, Ax-Alg can well tolerate the conditions in the mouth, stomach and small intestine and reach the colon where Ax was released due to fermentation of gut microbiota. Mice experiment showed that Ax-Alg reduced dextran sulfate sodium-induced colitis, involving weight loss, disease activity index, colonic mucosal integrity and inflammation, and oxidative damage. On the other hand, Ax-Alg regulated the gut microbiota composition and reduced the abundances of Bacteroidetes members that had positive correlation with ulcerative colitis. Ax-Alg had better effect on the treatment of ulcerative colitis than oil-in-water emulsion, which can be attributed to the synergistic effect of Ax and alginate. This study can be helpful for the application of colon-targeted delivery system in the foods and treatment of colon diseases.

Distinct N and C Cross-Feeding Networks in a Synthetic Mouse Gut Consortium.

ABSTRACTThe complex interactions between the gut microbiome and host or pathogen colonization resistance cannot be understood solely from community composition. Missing are causal relationships, such as metabolic interactions among species, to better understand what shapes the microbiome. Here, we focused on metabolic niches generated and occupied by the Oligo-Mouse-Microbiota (OMM) consortium, a synthetic community composed of 12 members that is increasingly used as a model for the mouse gut microbiome. Combining monocultures and spent medium experiments with untargeted metabolomics revealed broad metabolic diversity in the consortium, constituting a dense cross-feeding network with more than 100 pairwise interactions. Quantitative analysis of the cross-feeding network revealed distinct C and N food webs, highlighting the two Bacteroidetes members Bacteroides caecimuris and Muribaculum intestinale as primary suppliers of carbon and a more diverse group as nitrogen providers. Cross-fed metabolites were mainly carboxylic acids, amino acids, and the so far not reported nucleobases. In particular, the dicarboxylic acids malate and fumarate provided a strong physiological benefit to consumers, presumably used in anaerobic respiration. Isotopic tracer experiments validated the fate of a subset of cross-fed metabolites, such as the conversion of the most abundant cross-fed compound succinate to butyrate. Thus, we show that this consortium is tailored to produce the anti-inflammatory metabolite butyrate. Overall, we provide evidence for metabolic niches generated and occupied by OMM members that lays a metabolic foundation to facilitate an understanding of the more complex in vivo behavior of this consortium in the mouse gut.IMPORTANCE This article maps out the cross-feeding network among 10 members of a synthetic consortium that is increasingly used as the model mouse gut microbiota. Combining metabolomics with in vitro cultivations, two dense networks of carbon and nitrogen exchange are described. The vast majority of the ∼100 interactions are synergistic in nature, in several cases providing distinct physiological benefits to the recipient species. These networks lay the groundwork toward understanding gut community dynamics and host-gut microbe interactions.

Shift and interaction of intestinal bacterial community in juvenile Chinese mitten crab Eriocheir sinensis upon astaxanthin feeding

Intestinal bacterial communities of juvenile Chinese mitten crab Eriocheir sinensis are investigated for the effects of dietary supplementation with different amounts of micro-algal astaxanthin (0, 30, 60, 90, and 120 mg/kg dry diet) and for the correlation to crab hemolymph antioxidant capacity and immunity. Comprehensively analyzing of bacterial 16S rRNA gene amplicons showed that astaxanthin supplement, particularly of 90 mg/kg, appeared to enrich especially the number of Bacteroidetes members, albeit not significantly, increased the relative abundance of Dysgonomonas sp. (OTU1156), and significantly decreased the relative abundance of Jinshanibacter sp. (OTU1324) (P < 0.05). Both Dysgonomonas sp. (OTU1156) and Jinshanibacter sp. (OTU1324) are dominant and native bacterial lineages, present in neither the farming water nor feed. The Dysgonomonas sp. (OTU1156) are probably probiotics involving the digesting of food rich in plant matter, while the Jinshanibacter sp. (OTU1324) are potential parasitic/pathogenic bacteria. Intestinal bacterial communities were improved for the metabolic capacity by astaxanthin, such as the ability to digest xenobiotics, which significantly correlates with the total antioxidant capacity (P < 0.05) of crab hemolymph. These findings contribute to better understanding of the mutual-interaction among astaxanthin, gut bacterial community structure, and hemolymph antioxidant capability and immunity, and shed light on the health and disease-resistance aquaculture of crabs.

Characteristic Changes of Bioaerosols in Beijing and Tsogt-Ovoo During Dust Events

Dust events moving at high altitudes by westerly wind can transport aerosols from Asian deserts to eastern Asia deposition areas such as China. Aerosols do not include only mineral particles but also microbial particles, which are called bioaerosols, and impact the ecosystem and air environment of the deposition area. For identifying the airborne microbial communities transported from the source area to the deposition area, bioaerosol samples were collected in the typical source region (Tsogt-Ovoo in Gobi deserts) and the deposition region (Beijing in Chinese industrial area) during dust events and non-dust days and the sampling sites were compared. The microscopic observation using DAPI fluorescent techniques revealed that the concentration of bioaerosols increased during the dust events in both the source and deposition regions. For the community structures of airborne bacteria at both sites, the dust-event occurrences changed the structure of the bacterial community and increased the diversity of bacterial communities during dust events. Some specific bacterial populations, such as members of Bacteroidetes, dominated during dust events. There is the possibility that specific bacteria can be maintained for a longer time in the atmosphere and might be transported from the source area to the deposition area.

Consistent Prebiotic Effects of Carrot RG-I on the Gut Microbiota of Four Human Adult Donors in the SHIME® Model despite Baseline Individual Variability.

The human gut microbiome is currently recognized to play a vital role in human biology and development, with diet as a major modulator. Therefore, novel indigestible polysaccharides that confer a health benefit upon their fermentation by the microbiome are under investigation. Based on the recently demonstrated prebiotic potential of a carrot-derived pectin extract enriched for rhamnogalacturonan I (cRG-I), the current study aimed to assess the impact of cRG-I upon repeated administration using the M-SHIME technology (3 weeks at 3g cRG-I/d). Consistent effects across four simulated adult donors included enhanced levels of acetate (+21.1 mM), propionate (+17.6 mM), and to a lesser extent butyrate (+4.1 mM), coinciding with a marked increase of OTUs related to Bacteroides dorei and Prevotella species with versatile enzymatic potential likely allowing them to serve as primary degraders of cRG-I. These Bacteroidetes members are able to produce succinate, explaining the consistent increase of an OTU related to the succinate-converting Phascolarctobacterium faecium (+0.47 log10(cells/mL)). While the Bifidobacteriaceae family remained unaffected, a specific OTU related to Bifidobacterium longum increased significantly upon cRG-I treatment (+1.32 log10(cells/mL)). Additional monoculture experiments suggested that Bifidobacterium species are unable to ferment cRG-I structures as such and that B. longum probably feeds on arabinan and galactan side chains of cRG-I, released by aforementioned Bacteroidetes members. Overall, this study confirms the prebiotic potential of cRG-I and additionally highlights the marked consistency of the microbial changes observed across simulated subjects, suggesting the involvement of a specialized consortium in cRG-I fermentation by the human gut microbiome.