Selective impact of three homogenous polysaccharides with different structural characteristics from Grifola frondosa on human gut microbial composition and the structure-activity relationship

Natural polysaccharides interact with gut microbes to enhance human well-being. Grifola frondosa is a polysaccharides-rich edible and medicinal mushroom. The prebiotic potential of G. frondosa polysaccharides has been explored in recent years, however, the relationship between their various structural features and prebiotic activities is poorly understood. In this study, three homogenous polysaccharides GFP10, GFP21 and GFP22 having different molecular weights (Mw), monosaccharide compositions and glycosidic linkages were purified from G. frondosa, and their effects on intestinal microbial composition were compared. GFP10 was a fucomannogalactan with an Mw of 23.0 kDa, and it selectively inhibited Enterobacter, while GFP21 was a fucomannogalactoglucan with an Mw of 18.6 kDa, and it stimulated Catenibacterium. GFP22 was a 4.9 kDa mannoglucan that selectively inhibited Klebsiella and boosted Bifidobacterium, Catenibacterium and Phascolarctobacterium, and prominently promoted the production of short-chain fatty acids (SCFAs). The selective modulation of gut microbiota by polysaccharides was structure-dependent. A relatively lower Mw and a high proportion of glycosidic linkages like T-Glcp, 1,3-Glcp, 1,3,6-Glcp and 1,4-Glcp might be more easily utilized to produce SCFAs and beneficial for the proliferation of Catenibacterium and Phascolarctobacterium. This research provided a valuable resource for further exploring the structure-activity relationship and prebiotic activity of G. frondosa polysaccharides.

Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases

BACKGROUND

Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phenotypic and genotypic approaches, we studied the changes in the bacterial, phage and fungal components of the microbiota as well as the metabolome and the β-lactamase activity of the stools. This allowed assessing their degrees of perturbation and resilience.

RESULTS

While only two subjects had detectable concentrations of antibiotics in their faeces, suggesting important antibiotic degradation in the gut, the intravenous treatment perturbed very significantly the bacterial and phage microbiota, as well as the composition of the metabolome. In contrast, treatment impact was relatively low on the fungal microbiota. At the end of the surveillance period, we found evidence of resilience across the gut system since most components returned to a state like the initial one, even if the structure of the bacterial microbiota changed and the dynamics of the different components over time were rarely correlated. The observed richness of the antibiotic resistance genes repertoire was significantly reduced up to day 30, while a significant increase in the relative abundance of β-lactamase encoding genes was observed up to day 10, consistent with a concomitant increase in the β-lactamase activity of the microbiota. The level of β-lactamase activity at baseline was positively associated with the resilience of the metabolome content of the stools.

CONCLUSIONS

In healthy adults, antibiotics perturb many components of the microbiota, which return close to the baseline state within 30 days. These data suggest an important role of endogenous β-lactamase-producing anaerobes in protecting the functions of the microbiota by de-activating the antibiotics reaching the colon. Video Abstract.

The hidden threat: Environmental toxins and their effects on gut microbiota

The human gut microbiota (GM), which consists of a complex and diverse ecosystem of bacteria, plays a vital role in overall wellness. However, the delicate balance of this intricate system is being compromised by the widespread presence of environmental toxins. The intricate connection between contaminants in the environment and human well-being has garnered significant attention in recent times. Although many environmental pollutants and their toxicity have been identified and studied in laboratory settings and animal models, there is insufficient data concerning their relevance to human physiology. Consequently, research on the toxicity of environmental toxins in GM has gained prominence in recent years. Various factors, such as air pollution, chemicals, heavy metals, and pesticides, have a detrimental impact on the composition and functioning of the GM. This comprehensive review aims to comprehend the toxic effects of numerous environmental pollutants, including antibiotics, endocrine-disrupting chemicals, heavy metals, and pesticides, on GM by examining recent research findings. The current analysis concludes that different types of environmental toxins can lead to GM dysbiosis and have various potential adverse effects on the well-being of animals. We investigate the alterations to the GM composition induced by contaminants and their impact on overall well-being, providing a fresh perspective on research related to pollutant exposure.

A Millifluidic Chamber for Controlled Shear Stress Testing: Application to Microbial Cultures

In vitro platforms such as bioreactors and microfluidic devices are commonly designed to engineer tissue models as well as to replicate the crosstalk between cells and microorganisms hosted in the human body. These systems promote nutrient supply and waste removal through culture medium recirculation; consequently, they intrinsically expose cellular structures to shear stress, be it a desired mechanical stimulus to drive the cell fate or a potential inhibitor for the model maturation. Assessing the impact of shear stress on cellular or microbial cultures thus represents a crucial step to define proper environmental conditions for in vitro models. In this light, the aim of this study was to develop a millifluidic device enabling to generate fully controlled shear stress profiles for quantitatively probing its influence on tissue or bacterial models, overcoming the limitations of previous reports proposing similar devices. Relying on this millifluidic tool, we present a systematic methodology to test how adherent cellular structures react to shear forces, which was applied to the case of microbial biofilms as a proof of concept. The results obtained suggest our approach as a suitable testbench to evaluate culture conditions in terms of shear stress faced by cells or microorganisms.

Alterations in the intestinal microbiota associated with active tuberculosis and latent tuberculosis infection

Objectives

To study the characteristics of intestinal microbiota at different stages of Mycobacterium tuberculosis infection.

Methods

Fecal samples of 19 active tuberculosis (ATB) patients, 21 latent tuberculosis infection (LTBI) individuals, and 20 healthy controls (HC) were collected. Gut microbiota of all the participants were analyzed by 16S rDNA sequencing. Clinical information of ATB patients was also collected and analyzed.

Results

Both ATB and LTBI groups showed significant decreases in microbial diversity and decline of Clostridia. For ATB patients, bacteria within phylum Proteobacteria increased. While for LTBI individuals, genera Prevotella and Rosburia enriched. The abundance of Faecalibacterium, Clostridia and Gammaproteobacteria has the potential to diagnose ATB, with the area under the curve (AUC) of 0.808, 0.784 and 0.717. And Prevotella and Rosburia has the potential to diagnose LTBI, with the AUC of 0.689 and 0.689. Notably, in ATB patients, the relative abundance of Blautia was negatively correlated with the proportions of peripheral T cells and CD8+T cells. And serum direct bilirubin was positively correlated with Bacteroidales, while negatively correlated with Clostridiales in ATB patients.

Conclusions

The specifically changed bacteria are promising markers for ATB and LTBI diagnosis. Some gut bacteria contribute to anti-MTB immunity through interactions with T cells and bilirubin.

A structure defined pectin SA02B from Semiaquilegia adoxoides is metabolized by human gut microbes

Polysaccharide is one of the major factors for shaping the gut microbiota. However, bioactivity of polysaccharide isolated from Semiaquilegia adoxoides on human gut microbiota remains unclear. Thus, we hypothesize gut microbes may act on it. Herein, pectin SA02B from the roots of Semiaquilegia adoxoides with molecular weight 69.26 kDa was elucidated. The backbone of SA02B was composed of alternate 1, 2-linked α-Rhap and 1, 4-linked α-GalpA, with branches of terminal (T) -, 1, 4-, 1, 3- and 1, 3, 6-linked β-Galp, T-, 1, 5- and 1, 3, 5-linked α-Araf and T-, 1, 4-linked-β-Xylp substituted at C-4 of 1, 2, 4-linked α-Rhap. Bioactivity screening showed SA02B promoted the growth of Bacteroides spp. which deconstructed it into monosaccharide. Simultaneously, we observed competition might exist between Bacteroides spp. and probiotics. Besides, we found that both Bacteroides spp. and probiotics could generate SCFAs grown on SA02B. Our findings highlight SA02B may deserve as a prebiotic to be explored to benefit the health gut microbiota.

Gut bacterial alginate degrading enzymes

Alginates are abundant marine anionic polysaccharides consumed by humans. Thus, over the years some understanding has emerged about alginate utilization by human gut microbiota (HGM). However, insights have been obtained only recently at the molecular level with regard to structure and function of alginate degrading and metabolizing enzymes from HGM. Still, numerous studies report on effects of alginates on bacterial communities from digestive tracts of various, predominantly marine organisms feeding on alginate and some of the involved alginate lyases have been characterized. Other studies describe the beneficial impact on gut microbiota elicited by alginates in animal models, for example, high-fat-diet-fed mice addressing obesity or as feed supplements for livestock. Alginates are depolymerized by a β-elimination reaction catalyzed by polysaccharide lyases (PLs) referred to as alginate lyases (ALs). The ALs are found in 15 of the 42 PL families categorized in the CAZy database. While genome mining has led to prediction of ALs encoded by bacteria of the HGM; currently, only four enzymes from this niche have been characterized biochemically and two crystal structures are reported. Alginates are composed of mannuronate (M) and guluronate (G) residues organized in M-, G-, and MG-blocks, which calls for ALs of complementary specificity to effectively depolymerize alginate to alginate oligosaccharides (AOSs) and monosaccharides. Typically, ALs of different PL families are encoded by genes arranged in clusters denoted as polysaccharide utilization loci. Currently, biochemical and structural analyses of marine bacterial ALs contribute to depicting the mode of action of predicted enzymes from bacteria of the HGM.

Structure characterization of a highly branched galactan from the slug Vaginulus alte and its utilization by human gut microbiota

The slug Vaginulus alte is used as folk medicine in China, but the structure and activities of its galactan components remain to be clarified. Here, the galactan from V. alte (VAG) was purified. The Mw of VAG was determined as ~28.8 kDa. Chemical composition analysis showed that VAG was composed of d-galactose (75 %) and l-galactose (25 %). To elucidate its precise structure, a series of disaccharides and trisaccharides were purified from mild acid hydrolyzed VAG and their structures were characterized by 1D/2D NMR spectroscopy. Based on methylation analysis and structural analysis of oligosaccharides, VAG was elucidated as a highly branched polysaccharide and mainly composed of (1 → 6)- or (1 → 3)-linked β-d-galactose, and distinct (1 → 2)-linked α-l-galactose. The investigation of probiotic effects in vitro revealed that VAG could promote the growth of B. thetaiotaomicron and B. ovatus, while had no effect on the growth of L. acidophilus, L. rhamnosus, B. longum subsp. infantis and B. animalis subsp. lactis, but dVAG-3 with Mw ~1.0 kDa could promote the growth of L. acidophilus. These results will provide insights into specific structures and functions of polysaccharides from the V. alte.

Deciphering the antibiotic resistome and microbial community in municipal wastewater treatment plants at different elevations in eastern and western China

Antibiotic resistance genes (ARGs) as emerging environmental contaminants pose severe global risks to public health and ecosystems. Municipal wastewater treatment plants (WWTPs) are crucial transmitters for the dissemination and propagation of ARGs into receiving water bodies via mobile genetic elements (MGEs). However, the comprehensive and deep deciphering of the diversity, abundance, and potential hosts of ARGs in two distinct altitudinal WWTPs is scarce. In this work, we revealed the elevational distribution characteristics of the resistance genes and microbial community of six WWTPs from two distinct geographical zones: a low-elevation (LE) region (Shandong, 10-22 m above sea level) and a high-elevation (HE) region (Gansu, 1,520-1,708 m above sea level). Significant elevational variations in the diversity and relative abundance of resistance genes were observed. Wastewater treatment could significantly reduce the concentrations of ARGs and MGEs by about 1-2 and 2-3 orders of magnitude, respectively. However, above 69.95% of resistance genes were enriched in effluent. In particular, 24 ARG subtype, 3 MGE subtypes, and 59 bacterial genera were persistent in all samples. More potential hosts for ARGs in LE region and more abundant human gut microbiota in HE region were identified. This work provides helpful information for controlling the spread of ARGs for their management and assessment, thereby mitigating the risks of ARGs in WWTPs.

In vitro human gut microbiota fermentation models: opportunities, challenges, and pitfalls

The human gut microbiota (HGM) plays a pivotal role in health and disease. Consequently, nutritional and medical research focusing on HGM modulation strategies as a means of improving host health is steadily increasing. In vitro HGM fermentation models offer a valid complement to human and animal studies when it comes to the mechanistic exploration of novel modulation approaches and their direct effects on HGM composition and activity, while excluding interfering host effects. However, in vitro cultivation of HGM can be challenging due to its high oxygen sensitivity and the difficulties of accurately modeling the physio-chemical complexity of the gut environment. Despite the increased use of in vitro HGM models, there is no consensus about appropriate model selection and operation, sometimes leading to major deficiencies in study design and result interpretation. In this review paper, we aim to analyze crucial aspects of the application, setup and operation, data validation and result interpretation of in vitro HGM models. When carefully designed and implemented, in vitro HGM modeling is a powerful strategy for isolating and investigating biotic and abiotic factors in the HGM, as well as evaluating their effects in a controlled environment akin to the gut. Furthermore, complementary approaches combining different in vitro and in vivo models can strengthen the design and interpretation of human studies.

The structure of a Bacteroides thetaiotaomicron carbohydrate-binding module provides new insight into the recognition of complex pectic polysaccharides by the human microbiome

The Bacteroides thetaiotaomicron has developed a consortium of enzymes capable of overcoming steric constraints and degrading, in a sequential manner, the complex rhamnogalacturonan II (RG-II) polysaccharide. BT0996 protein acts in the initial stages of the RG-II depolymerisation, where its two catalytic modules remove the terminal monosaccharides from RG-II side chains A and B. BT0996 is modular and has three putative carbohydrate-binding modules (CBMs) for which the roles in the RG-II degradation are unknown. Here, we present the characterisation of the module at the C-terminal domain, which we designated BT0996-C. The high-resolution structure obtained by X-ray crystallography reveals that the protein displays a typical β-sandwich fold with structural similarity to CBMs assigned to families 6 and 35. The distinctive features are: 1) the presence of several charged residues at the BT0996-C surface creating a large, broad positive lysine-rich patch that encompasses the putative binding site; and 2) the absence of the highly conserved binding-site signatures observed in CBMs from families 6 and 35, such as region A tryptophan and region C asparagine. These findings hint at a binding mode of BT0996-C not yet observed in its homologues. In line with this, carbohydrate microarrays and microscale thermophoresis show the ability of BT0996-C to bind α1-4-linked polygalacturonic acid, and that electrostatic interactions are essential for the recognition of the anionic polysaccharide. The results support the hypothesis that BT0996-C may have evolved to potentiate the action of BT0996 catalytic modules on the complex structure of RG-II by binding to the polygalacturonic acid backbone sequence.

The claim of primacy of human gut Bacteroides ovatus in dietary cellobiose degradation

A demonstration of cellulose degrading bacterium from human gut changed our view that human cannot degrade the cellulose. However, investigation of cellulose degradation by human gut microbiota on molecular level has not been completed so far. We showed here, using cellobiose as a model that promoted the growth of human gut key members, such as Bacteroides ovatus (BO), to clarify the molecular mechanism. Our results showed that a new polysaccharide utilization locus (PUL) from BO was involved in the cellobiose capturing and degradation. Further, two new cellulases BACOVA_02626^GH5 and BACOVA_02630^GH5 on the cell surface performed the degradation of cellobiose into glucose were determined. The predicted structures of BACOVA_02626^GH5 and BACOVA_02630^GH5 were highly homologous with the cellulase from soil bacteria, and the catalytic residues were highly conservative with two glutamate residues. In murine experiment, we observed cellobiose reshaped the composition of gut microbiota and probably modified the metabolic function of bacteria. Taken together, our findings further highlight the evidence of cellulose can be degraded by human gut microbes and provide new insight in the field of investigation on cellulose.

Functions and specificity of bacterial carbohydrate sulfatases targeting host glycans

Sulfated host glycans (mucin O-glycans and glycosaminoglycans [GAGs]) are critical nutrient sources and colonisation factors for Bacteroidetes of the human gut microbiota (HGM); a complex ecosystem comprising essential microorganisms that coevolved with humans to serve important roles in pathogen protection, immune signalling, and host nutrition. Carbohydrate sulfatases are essential enzymes to access sulfated host glycans and are capable of exquisite regio- and stereo-selective substrate recognition. In these enzymes, the common recognition features of each subfamily are correlated with their genomic and environmental context. The exo-acting carbohydrate sulfatases are attractive drug targets amenable to small-molecule screening and subsequent engineering, and their high specificity will help elucidate the role of glycan sulfation in health and disease. Inhibition of carbohydrate sulfatases provides potential routes to control Bacteroidetes growth and to explore the influence of host glycan metabolism by Bacteroidetes on the HGM ecosystem. The roles of carbohydrate sulfatases from the HGM organism Bacteroides thetaiotaomicron and the soil isolated Pedobacter heparinus (P. heparinus) in sulfated host glycan metabolism are examined and contrasted, and the structural features underpinning glycan recognition and specificity explored.

Metabolic profile and dynamic characteristic of rhubarb during the vitro biotransformation by human gut microbiota

Rhubarb is a popular food in the world with laxative effects and steamed pieces of rhubarb (SP) have been widely applied to treatment of constipation in China due to its safety and effectiveness. In the study, metabolism in vitro was conducted to study influence of gut microbiota between raw pieces of rhubarb (RP) and SP. The results showed obvious classifications in metabolic profile between RP and SP were revealed by chemometric analysis, and prompted gut microbiota affected metabolism of rhubarb. Furthermore, 16 characteristic components were identified to distinguish the differences in metabolism. Finally, quantitative analysis of 14 components were verified the regulation of gut microbiota on rhubarb and discovered concentration of components affected the rate of metabolism. The study indicated regulation by gut microbiota could be probably responsible for differences of laxative effects between RP and SP, providing new perspective for exploring mechanisms of effectiveness in clinical application for SP.

Nano-Al2O3 particles affect gut microbiome and resistome in an in vitro simulator of the human colon microbial ecosystem

Nano-Al₂O₃ has been widely used in various consumer products and water treatment processes because of its unique physicochemical properties. The probability of human exposure to nano-Al₂O₃ increases significantly, of which oral ingestion is an important route. However, effects and underlying mechanisms of nano-Al₂O₃ on gut microbiota and resistome are still not well delineated. Here, we systematically investigated the effects of nano-Al₂O₃ on the human gut microbiome by an in vitro simulator of human colon microbial ecosystem. Results indicated that nano-Al₂O₃ interfered with the gut microbiota, and significantly suppressed the short-chain fatty acids metabolism, which might pose adverse effects on the host. More seriously, high level of nano-Al₂O₃ (50 mg/L) was more destructive to the gut flora, though the damage might be temporary. In addition, sub-inhibitory low-dose of nano-Al₂O₃ (0.1 mg/L) significantly enhanced the abundance of antibiotic resistance genes (ARGs) after 7-day exposure. This is attributed to that low concentration of nano-Al₂O₃ can promote horizontal transfer of ARGs by increasing cell membrane permeability and relative abundance of transposase (e.g. tnpA, IS613, and Tp614). Our findings confirmed the adverse effects of nano-Al₂O₃ on the human gut resistome and emphasized the necessity to assess potential risks of nanomaterials on the human gut health.

1H, 13C, 15N resonance assignment of the enzyme KdgF from Bacteroides eggerthii

To fully utilize carbohydrates from seaweed biomass, the degradation of the family of polysaccharides known as alginates must be understood. A step in the degradation of alginate is the conversion of 4,5-unsaturated monouronates to 4-deoxy-L-erythro-5-hexoseulose catalysed by the enzyme KdgF. In this study BeKdgF from Bacteroides eggerthii from the human gut microbiota has been produced isotopically labelled in Escherichia coli. Here the ¹H, ¹³C, and ¹⁵N NMR chemical shift assignment for BeKdgF is reported.

Draft genomes and descriptions of Urmitella timonensis gen. nov., sp. nov. and Marasmitruncus massiliensis gen. nov., sp. nov., isolated from severely malnourished African children using culturomics

Two strains, designated as Marseille-P2918^T and Marseille-P3646^T, were isolated from a 14-week-old Senegalese girl using culturomics: Urmitella timonensis strain Marseille-P2918^T (= CSUR P2918, = DSM 103634) and Marasmitruncus massiliensis strain Marseille-P3646^T (= CSUR P3646, = CCUG72353). Both strains were rod-shaped, anaerobic, spore forming motile bacteria. The 16S rRNA gene sequences of strains Marseille-P2918^T (LT598554) and Marseille-P3646^T (LT725660) shared 93.25% and 94.34% identity with Tissierella praeacuta ATCC 25539^T and Anaerotruncus colihominis CIP 107754^T, their respective phylogenetically closest species with standing in nomenclature. Therefore, strain Marseille-P2918^T is classified within the family Tissierellaceae and order Tissierellales whereas strain Marseille-P3646^T is classified within the family Oscillospiraceae and order Eubacteriales. The genome of strain Marseille-P2918^T had a size of 2.13 Mb with a GC content of 50.52% and includes six scaffolds and six contigs, and that of strain Marseille-P3646^T was 3.76 Mbp long consisting of five contigs with a 50.04% GC content. The genomes of both strains presented a high percentage of genes encoding enzymes involved in genetic information and processing, suggesting a high growth rate and adaptability. These new taxa are extensively described and characterised in this paper, using the concept of taxono-genomic description.

Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria

Lactate accumulation in the human gut is linked to a range of deleterious health impacts. However, lactate is consumed and converted to the beneficial short-chain fatty acids butyrate and propionate by indigenous lactate-utilizing bacteria. To better understand the underlying genetic basis for lactate utilization, transcriptomic analyses were performed for two prominent lactate-utilizing species from the human gut, Anaerobutyricum soehngenii and Coprococcus catus, during growth on lactate, hexose sugar or hexose plus lactate. In A. soehngenii L2-7 six genes of the lactate utilization (lct) cluster, including NAD-independent d-lactate dehydrogenase (d-iLDH), were co-ordinately upregulated during growth on equimolar d- and l-lactate (dl-lactate). Upregulated genes included an acyl-CoA dehydrogenase related to butyryl-CoA dehydrogenase, which may play a role in transferring reducing equivalents between reduction of crotonyl-CoA and oxidation of lactate. Genes upregulated in C. catus GD/7 included a six-gene cluster (lap) encoding propionyl CoA-transferase, a putative lactoyl-CoA epimerase, lactoyl-CoA dehydratase and lactate permease, and two unlinked acyl-CoA dehydrogenase genes that are candidates for acryloyl-CoA reductase. A d-iLDH homologue in C. catus is encoded by a separate, partial lct, gene cluster, but not upregulated on lactate. While C. catus converts three mols of dl-lactate via the acrylate pathway to two mols propionate and one mol acetate, some of the acetate can be re-used with additional lactate to produce butyrate. A key regulatory difference is that while glucose partially repressed lct cluster expression in A. soehngenii, there was no repression of lactate-utilization genes by fructose in the non-glucose utilizer C. catus. This suggests that these species could occupy different ecological niches for lactate utilization in the gut, which may be important factors to consider when developing lactate-utilizing bacteria as novel candidate probiotics.

Imaging the in vivo growth patterns of bacteria in human gut Microbiota

How to study the unculturable bacteria in the laboratory is one of the major challenges in human gut microbiota research. The resulting lack of microbiology knowledge of this "dark matter" greatly hinders further understanding of our gut microbiota. Here, to characterize the in vivo growth and division of human gut bacteria, we report the integrative use of STAMP (sequential tagging with D-amino acid-based metabolic probes) and fluorescence in situ hybridization (FISH) in a human microbiota-associated mouse model. After stable colonization of the human fecal microbiotas in germ-free mice, two fluorescent D-amino acid probes were sequentially administered by gavage, and the dually labeled peptidoglycan of the bacteria provided a chronological recording of their cell wall syntheses. Following taxonomic identification with FISH staining, the growth patterns of 32 species, including 5 currently unculturables, were identified. Surprisingly, we found that many bacterial species in the human microbiota were significantly shorter than those in the mouse gut microbiota. An imaging database for gut bacteria ̶ Microbiome Atlas was built for summarizing STAMP imaging of bacteria from different microbiotas, which can be contributed by the microbiota research community worldwide. This integrative imaging strategy and the database will promote our understanding of the bacterial cytology in gut microbiotas and facilitate communications among cellular microbiologists.

Running after ghosts: are dead bacteria the dark matter of the human gut microbiota?

The human gut microbiota has been explored by a wide range of culture-dependent and culture-independent methods, revealing that many microbes remain uncharacterized and uncultured. In this work, we aimed to confirm the hypothesis that some of the species present in the human gut microbiota remain uncultured not because of culture limitations, but because all members of such species are dead before reaching the end of the gastro-intestinal tract.We evaluate this phenomenon by studying the microbial viability and culturability of the human gut microbiota from the fresh fecal materials of eight healthy adults. For the first time, we applied fluorescence-activated cell sorting (FACS) combined with 16S metagenomics analysis and microbial culturomics.We identified a total of 1,020 bacterial OTUs and 495 bacterial isolates through metagenomics and culturomics, respectively. Among the FACS metagenomics results, only 735 bacterial OTUs were alive, comprising on average 42% of known species and 87% of relative abundance per individual. The remaining uncultured bacteria were rare, dead, or injured.Our strategy allowed us to shed light on the dark matter of the human gut microbiota and revealed that both metagenomics and culturomics approaches are needed for greater insight into the diversity and richness of bacteria in the human gut microbiota. Further work on culture is needed to enhance the repertoire of cultured gut bacteria by targeting low abundance bacteria and optimizing anaerobic sample conditioning and processing to preserve the viability of bacteria.

Discrete genetic loci in human gut Bacteroides thetaiotaomicron confer pectin metabolism

Although the polysaccharide utilization loci (PULs) activated by pectin have been defined, due to the complex of side-chain structure, the degradative mechanisms still remain vague. Thus, we hypothesize that there may have other specific PULs to target pectin. Here, we characterize loci-encoded proteins expressed by Bacteroides thetaiotaomicron (BT) that are involved in the pectin capturing, importation, de-branching and degradation into monosaccharides. Totally, four PULs contain ten enzymes and four glycan binding proteins which including a novel surface enzyme and a surface glycan binding protein are identified. Notably, PUL2 and PUL3 have not been reported so far. Further, we show that the degradation products support the growth of other Bacteroides spp. and probiotics. In addition, genes involved in this process are conservative in other Bacteroides spp. Our results further highlight the contribution of Bacteroides spp. to metabolism the pectic network.

The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome

BACKGROUND

Biogenic histamine plays an important role in immune response, neurotransmission, and allergic response. Although endogenous histamine production has been extensively studied, the contributions of histamine produced by the human gut microbiota have not been explored due to the absence of a systematic annotation of histamine-secreting bacteria.

RESULTS

To identify the histamine-secreting bacteria from in the human gut microbiome, we conducted a systematic search for putative histamine-secreting bacteria in 36,554 genomes from the Genome Taxonomy Database and Unified Human Gastrointestinal Genome catalog. Using bioinformatic approaches, we identified 117 putative histamine-secreting bacteria species. A new three-component decarboxylation system including two colocalized decarboxylases and one transporter was observed in histamine-secreting bacteria among three different phyla. We found significant enrichment of histamine-secreting bacteria in patients with inflammatory bowel disease but not in patients with colorectal cancer suggesting a possible association between histamine-secreting bacteria and inflammatory bowel disease.

CONCLUSIONS

The findings of this study expand our knowledge of the taxonomic distribution of putative histamine-secreting bacteria in the human gut.

Optimisation of sample storage and DNA extraction for human gut microbiota studies​

Background

New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important.

Results

Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution.

Conclusions

Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02233-y.

The use of an in-vitro batch fermentation (human colon) model for investigating mechanisms of TMA production from choline, L-carnitine and related precursors by the human gut microbiota

Purpose

Plasma trimethylamine-N-oxide (TMAO) levels have been shown to correlate with increased risk of metabolic diseases including cardiovascular diseases. TMAO exposure predominantly occurs as a consequence of gut microbiota-dependent trimethylamine (TMA) production from dietary substrates including choline, carnitine and betaine, which is then converted to TMAO in the liver. Reducing microbial TMA production is likely to be the most effective and sustainable approach to overcoming TMAO burden in humans. Current models for studying microbial TMA production have numerous weaknesses including the cost and length of human studies, differences in TMA(O) metabolism in animal models and the risk of failing to replicate multi-enzyme/multi-strain pathways when using isolated bacterial strains. The purpose of this research was to investigate TMA production from dietary precursors in an in-vitro model of the human colon.

Methods

TMA production from choline, l-carnitine, betaine and γ-butyrobetaine was studied over 24–48 h using an in-vitro human colon model with metabolite quantification performed using LC–MS.

Results

Choline was metabolised via the direct choline TMA-lyase route but not the indirect choline–betaine-TMA route, conversion of l-carnitine to TMA was slower than that of choline and involves the formation of the intermediate γ-BB, whereas the Rieske-type monooxygenase/reductase pathway for l-carnitine metabolism to TMA was negligible. The rate of TMA production from precursors was choline > carnitine > betaine > γ-BB. 3,3-Dimethyl-1-butanol (DMB) had no effect on the conversion of choline to TMA.

Conclusion

The metabolic routes for microbial TMA production in the colon model are consistent with observations from human studies. Thus, this model is suitable for studying gut microbiota metabolism of TMA and for screening potential therapeutic targets that aim to attenuate TMA production by the gut microbiota.

Trial registration number

NCT02653001 (http://www.clinicaltrials.gov), registered 12 Jan 2016.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00394-021-02572-6.

An in vitro model for microbial fructoselysine degradation shows substantial interindividual differences in metabolic capacities of human fecal slurries

Fructoselysine is formed upon heating during processing of food products, and being a key intermediate in advanced glycation end product formation considered to be potentially hazardous to human health. Human gut microbes can degrade fructoselysine to yield the short chain fatty acid butyrate. However, quantitative information on these biochemical reactions is lacking, and interindividual differences therein are not well established. Anaerobic incubations with pooled and individual human fecal slurries were optimized and applied to derive quantitative kinetic information for these biochemical reactions. Of 16 individuals tested, 11 were fructoselysine metabolizers, with V_max, K_m and kcat-values varying up to 14.6-fold, 9.5-fold, and 4.4-fold, respectively. Following fructoselysine exposure, 10 of these 11 metabolizers produced significantly increased butyrate concentrations, varying up to 8.6-fold. Bacterial taxonomic profiling of the fecal samples revealed differential abundant taxa for these reactions (e.g. families Ruminococcaceae, Christenellaceae), and Ruminococcus_1 showed the strongest correlation with fructoselysine degradation and butyrate production (ρ ≥ 0.8). This study highlights substantial interindividual differences in gut microbial degradation of fructoselysine. The presented method allows for quantification of gut microbial degradation kinetics for foodborne xenobiotics, and interindividual differences therein, which can be used to refine prediction of internal exposure.

The role of soil arsenic fractionation in the bioaccessibility, transformation, and fate of arsenic in the presence of human gut microbiota

Soil arsenic (As) fractionation and its bioaccessibility are two important factors in human health risk assessment. However, data related to the impact of As minerals on the bioaccessibility with human gut microbiota involvement are scarce. In this study, speciation analysis was determined using HPLC-ICP-MS and XANES after incubation with colon microbiota from human origin, in combination with sequential extraction. Significant increase of colon As bioaccessibility was contributed primarily from As associated with amorphous and crystalline Fe/Al (hydr)oxides. We found a high degree of transformation at higher bioaccessibility (ave. 40 % of total As), which was predominantly present as liquid-phase As. In contrast, As transformation occurred mainly in the solid phase at lower bioaccessibility (< 5%), especially for soils containing As-S species. XANES spectroscopy revealed that As(III) increased by about 20 % in soil residues. Finally, the excreted As may be predominantly in association with (alumino)silicate minerals by SEM-EDX. It inferred that the priority sequence in As transformation by human gut microbiota was dissolved As(V), As(V) sorbed to mineral surfaces, crystalline As(V)-bearing minerals and As sulfides. This study will shed new light on the role of As-bearing minerals in evaluating health risks from soil As exposure.

The gut microbiome of COVID-19 recovered patients returns to uninfected status in a minority-dominated United States cohort

To investigate the relationship between intestinal microbiota and SARS-CoV-2-mediated pathogenicity in a United States, majority African American cohort. We prospectively collected fecal samples from 50 SARS-CoV-2 infected patients, 9 SARS-CoV-2 recovered patients, and 34 uninfected subjects seen by the hospital with unrelated respiratory medical conditions (controls). 16S rRNA sequencing and qPCR analysis was performed on fecal DNA/RNA. The fecal microbial composition was found to be significantly different between SARS-CoV-2 patients and controls (PERMANOVA FDR-P = .004), independent of antibiotic exposure. Peptoniphilus, Corynebacterium and Campylobacter were identified as the three most significantly enriched genera in COVID-19 patients compared to controls. Actively infected patients were also found to have a different gut microbiota than recovered patients (PERMANOVA FDR-P = .003), and the most enriched genus in infected patients was Campylobacter, with Agathobacter and Faecalibacterium being enriched in the recovered patients. No difference in microbial community structure between recovered patients and uninfected controls was observed, nor a difference in alpha diversity between the three groups. 24 of the 50 COVID-19 patients (48%) tested positive via RT-qPCR for fecal SARS-CoV-2 RNA. A significant difference in gut microbial composition between SARS-CoV-2 positive and negative samples was observed, with Klebsiella and Agathobacter being enriched in the positive cohort. No significant associations between microbiome composition and disease severity was found. The intestinal microbiota is sensitive to the presence of SARS-CoV-2, with increased relative abundance of genera (Campylobacter, Klebsiella) associated with gastrointestinal (GI) disease. Further studies are needed to investigate the functional impact of SARS-CoV-2 on GI health.

Metagenomic 16S rDNA amplicon data of microbial diversity of guts in Vietnamese humans with type 2 diabetes and nondiabetic adults

Type 2 diabetes mellitus (T2DM) is an important public health problem. The knowledge of bacterial communities in the gut of Vietnamese patients with T2DM and non diabetic controls is still insufficient. We report in this article the 16S rDNA amplicon data of the gut microbiomes of Vietnamese patients with T2DM and nondiabetic controls carried out using the Illumina sequencing. This work included 7 patients and 7 controls. A total of 1,627,646 reads were obtained and a total of 13 phyla, 25 classes, 94 genera were revealed. The top three dominant bacterial phyla in all subjects were Firmicutes, Bacteroidetes and Proteobacteria. Significant differences in the relative abundances of the phylum Firmicutes and class Clostridia between patients and controls were observed, suggesting that the reducing of phylum Firmicutes and class Clostridia in the gut may be linked to obesity and T2DM. All sequencing libraries were deposited in the NCBI SRA as BioProject PRJNA668251. The datasets are needed to determine the association between the bacterial composition of the gut and the pathogenesis of T2DM in Vietnamese patients.

Gut microbiota and old age: Modulating factors and interventions for healthy longevity

Our gut microbiota is a complex and dynamic ecosystem with a paramount role in shaping our metabolic and immunological functions. Recent research suggests that aging may negatively affect the composition, diversity, and function of our microbiota mainly due to alterations in diet and immunologic reactivity (i.e. immunosenescence), and increased incidence of certain diseases and, therefore, increased exposure to certain medication (e.g. antibiotics, proton pump inhibitors). In turn, this aging-related gut dysbiosis may contribute to the initiation and/or progress of other metabolic diseases, and consequently, to a decrease in healthy longevity. On the positive side, promising therapeutic interventions, such as diet supplementation with prebiotics, probiotics and synbiotics, or fecal microbiota transplantation, aimed to counteract these aging-related deleterious consequences, could improve our health, and extend our healthy lifespan. In this context, the current review aims to assess the latest progress in identifying the key elements affecting the gut microbiota of the older adults and their mechanism of action, and the effectiveness of the therapeutic interventions aimed at restoring the diversity and healthy functions of the gut microbiota in older individuals.

Comparative methods for fecal sample storage to preserve gut microbial structure and function in an in vitro model of the human colon

In vitro gut models, such as the mucosal artificial colon (M-ARCOL), provide timely and cost-efficient alternatives to in vivo assays allowing mechanistic studies to better understand the role of human microbiome in health and disease. Using such models inoculated with human fecal samples may require a critical step of stool storage. The effects of preservation methods on microbial structure and function in in vitro gut models have been poorly investigated. This study aimed to assess the impact of three commonly used preserving methods, compared with fresh fecal samples used as a control, on the kinetics of lumen and mucus-associated microbiota colonization in the M-ARCOL model. Feces from two healthy donors were frozen 48 h at - 80 °C with or without cryoprotectant (10% glycerol) or lyophilized with maltodextrin and trehalose prior to inoculation of four parallel bioreactors (e.g., fresh stool, raw stool stored at - 80 °C, stool stored at - 80 °C with glycerol and lyophilized stool). Microbiota composition and diversity (qPCR and 16S metabarcoding) as well as metabolic activity (gases and short chain fatty acids) were monitored throughout the fermentation process (9 days). All the preservative treatments allowed the maintaining inside the M-ARCOL of a complex and functional microbiota, but considering stabilization time of microbial profiles and activities (and not technical constraints associated with the supply of frozen material), our results highlighted 48 h freezing at - 80 °C without cryoprotectant as the most efficient method. These results will help scientists to determine the most accurate method for fecal storage prior to inoculation of in vitro gut microbiome models. KEY POINTS: • In vitro ARCOL model reproduces luminal and mucosal human microbiome. • Short-term storage of fecal sample influences microbial stabilization and activity. • 48 h freezing at - 80°C: most efficient method to preserve microbial ecosystem. • Scientific and technical requirements: influencers of preservation method.

Investigating host-microbiome interactions by droplet based microfluidics

BACKGROUND

Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota.

RESULTS

Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired.

CONCLUSION

By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships. Video Abstract.

Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis

The link between the gut microbiota and metabolic syndrome (MetS) has attracted widespread attention. Christensenellaceae was recently described as an important player in human health, while its distribution and relationship with MetS in Chinese population is still unknown. This study sought to observe the association between Christensenellaceae and metabolic indexes in a large sample of residents in South China. A total of 4,781 people from the GGMP project were included, and the fecal microbiota composition of these individuals was characterized by 16S rRNA sequencing and analyzed the relation between Christensenellaceae and metabolism using QIIME (Quantitative Insight Into Microbial Ecology, Version 1.9.1). The results demonstrated that microbial richness and diversity were increased in the group with a high abundance of Christensenellaceae, who showed a greater complexity of the co-occurrence network with other bacteria than residents who lacked Christensenellaceae. The enriched bacterial taxa were predominantly represented by Oscillospira, Ruminococcaceae, RF39, Rikenellaceae and Akkermansia as the Christensenellaceae abundance increased, while the abundances of Veillonella, Fusobacterium and Klebsiella were significantly reduced. Furthermore, Christensenellaceae was negatively correlated with the pathological features of MetS, such as obesity, hypertriglyceridemia and body mass index (BMI). We found reduced levels of lipid biosynthesis and energy metabolism pathways in people with a high abundance of Christensenellaceae, which may explain the negative relationship between body weight and Christensenellaceae. In conclusion, we found a negative correlation between Christensenellaceae and MetS in a large Chinese population and reported the geographical distribution of Christensenellaceae in the GGMP study. The association data from this population-level research support the investigation of strains within Christensenellaceae as potentially beneficial gut microbes.

In vitro model insights into the role of human gut microbiota on arsenic bioaccessibility and its speciation in soils

The bioaccessibility of arsenic and its speciation are two important factors in assessing human health risks exposure to contaminated soils. However, the effects of human gut microbiota on arsenic bioaccessibility and its speciation are not well characterized. In this study, an improved in vitro model was utilized to investigate the bioaccessibility of arsenic in the digestive tract and the role of human gut microbiota in the regulation of arsenic speciation. For all soils, arsenic bioaccessibility from the combined in vitro model showed that it was <40% in the gastric, small intestinal and colon phases. This finding demonstrated that the common bioaccessibility approach assuming 100% bioaccessibility would overestimate the human health risks posed by contaminated soils. Further to this, the study showed that arsenic bioaccessibility was 22% higher in the active colon phase than that in the sterile colon phase indicating that human colon microorganisms could induce arsenic release from the solid phase. Only inorganic arsenic was detected in the gastric and small intestinal phases, with arsenate [As(V)] being the dominant arsenic species (74%-87% of total arsenic). Arsenic speciation was significantly altered by the active colon microbiota, which resulted in the formation of methylated arsenic species, including monomethylarsonic acid [MMA(V)] and dimethylarsinic acid [DMA(V)] with low toxicity, and a highly toxic arsenic species monomethylarsonous acid [MMA(III)]. Additionally, a high level of monomethylmonothioarsonic acid [MMMTA(V)] (up to 17% of total arsenic in the extraction solution) with unknown toxicological properties was also detected in the active colon phase. The formation of various organic arsenic species demonstrated that human colon microorganisms could actively metabolize inorganic arsenic into methylated arsenicals and methylated thioarsenicals. Such transformation should be considered when assessing the human health risks associated with oral exposure to soil.

The homogenous polysaccharide SY01-23 purified from leaf of Morus alba L. has bioactivity on human gut Bacteroides ovatus and Bacteroides cellulosilyticus

Function of mulberry leaf (Morus alba L.) polysaccharide has been reported on antitumor, immunostimulatory and anti-inflammatory effects. However, the bioactivity on human gut microbiota is unclear so far. Here, three homogenous polysaccharides named SY01-21, SY01-22, SY01-23 were isolated from mulberry leaf with molecular weight 57 kDa, 25 kDa and 7.2 kDa, respectively. The monosaccharide composition of SY01-21 contained rhamnose, galactose and arabinose in a molar ratio of 7.60:43.52:48.88. SY01-22 contained rhamnose, galacturonic acid, glucose, galactose, xylose and arabinose in a molar ratio of 14.61:9.06:1.35:34.65:2.99:37.34. SY01-23 contained rhamnose, glucuronic acid, galacturonic acid, glucose, galactose, xylose and arabinose in a molar ratio of 23.00:4.12:24.60:5.74:17.28:1.12:24.13. Bioactivity test showed SY01-21 promoted the growth of Bacteroides cellulosilyticus (BC) while SY01-22 benefited the growth of Bacteroides ovatus (BO). Interestingly, SY01-23 boosted the growth of both BO and BC. However, Bacteroides thetaiotamicron (BT) only grew on 5 mg/mL SY01-21. Intriguingly, the growth of co-culture of BT with BO or BC was better than monoculture. This suggested that cross-feeding might exist between them. Besides, we found BO and BC generated acetate and propionate by utilizing SY01-23. The above results suggested that SY01-23 might modify human gut microbiota by driving colonization of Bacteroides in the gut to improve wellness.

Multidisciplinary approach to determine the effect of polybrominated diphenyl ethers on gut microbiota

Environmental health is increasingly compromised by persistent toxic substances, which may have serious implications in food safety and, thus, in human health. Polybrominated diphenyl ethers (PBDEs) are anthropogenic contaminants with endocrine disruption abilities and are commonly found in seafood, the main route of human exposure. Growing evidence points out that the human gut microbiota interacts with xenobiotics, which may lead to impairment of host homeostasis if functions of microbiota become compromised. The aim of this study was to ascertain if the physiological balance of human gut microbiome is affected by the presence and degree of exposure to PBDEs. Fermentation was performed in a batch closed-system using an inoculum made from fresh human stool. The volatolomic profile was analysed by solid-phase microextraction coupled to gas chromatography-mass spectrometry. Mesophilic, Gram-negative bacteria and coliforms were quantified by classic plating methods. Changes in the gut microbiome were evaluated after DNA extraction followed by deep sequencing of the 16S rDNA region. The exposure to PBDEs resulted in an imbalance in sulfur, short-chain fatty acids and aromatic organic compounds, changing the microbial volatolome in a dose- and time-dependent manner. Slight deviations in the microbial structure of human gut occurred in the presence of PBDEs, especially for high doses of exposure. For the first time, the impact of PBDEs on the microbial homeostasis of human gut microbiota was taken into consideration, revealing noteworthy modifications with serious health implications even at oral exposure doses considered as safe by worldwide regulatory entities.

Draft genome and description of Negativicoccus massiliensis strain Marseille-P2082, a new species isolated from the gut microbiota of an obese patient

Strain Marseille-P2082, an anaerobic, non-motile, asporogenous, Gram-negative, coccoid bacterium was isolated from the faeces of a 33 year-old obese French woman before bariatric surgery. The isolate exhibits 98.65% 16S rRNA gene nucleotide sequence similarity with Negativicoccus succinicivorans strain ADV 07/08/06-B-1388^T, its current closest phylogenetic neighbour with standing in nomenclature. However, the dDDH relatedness between the new isolate and N. succinicivorans type strain ADV 07/08/06-B-1388^T is 52.5 ± 2.7%. Strain Marseille-P2082 has a genome of 1,360,589 bp with a 51.1% G+C content. Its major fatty acids were identified as C_18:1n9, C_18:0 and C_16:0. Based on its phenotypic, genomic and phylogenetic characteristics, strain Marseille-P2082^T [= CSURP2082 (Collection de Souches de l'Unité des Rickettsies) = DSM 100853] is proposed as the type strain of the novel species Negativicoccus massiliensis sp. nov. The 16S rRNA gene sequence and whole-genome shotgun sequence have been deposited in EMBL-EBI under accession numbers LN876651 and LT700188, respectively.

Lead bioaccessibility in farming and mining soils: The influence of soil properties, types and human gut microbiota

To better understand the risk assessment of Lead (Pb) in contaminated soils, 78 soil samples were collected from different locations in China and Pb bioaccessibility was assessed using the PBET (The Physiologically Based Extraction Test) method combined with SHIME (The Simulator of the Human Intestinal Microbial Ecosystem), and Pb bioaccessibility data from the PBET method on 88 soil samples that found in the literature were also used for the assessment. For all the soils, the mean Pb bioaccessibility was as follows: the gastric phase (31.25%) > colon phase (17.78%) > small intestinal phase (10.13%). The values of Pb bioaccessibility in most soils were lower than 60%, which is the typical default assumption for Pb (RBA, relatively bioavailability) by the US EPA. Mean Pb bioaccessibility (41.10% and 14.00% for gastric and small intestinal phases, respectively) in the present study was slightly higher than the values from the literature (24.80% and 8.68% for gastric and small intestinal phases, respectively) in the gastrointestinal tract. Mean Pb bioaccessibility was lower in acidic soil during the small intestinal phase, while the values for the alkaline soil were higher in the small intestinal and colon phases. In the gastric and small intestinal phases, mean Pb bioaccessibility in farming soils was slightly lower than it was in mining soils. However, the mean Pb bioaccessibility from farming soils was increased compared with mining soils in the colon phase given the action of human gut microbiota. Soil pH and type are important factors for predicting soil Pb bioaccessibility and health risk.

Gorillibacterium timonense sp. nov., isolated from an obese patient

A Gram-negative and facultative anaerobic bacterium, designated strain SN4^T, was isolated from the stool sample of an obese Amazonian patient. The new isolate was characterized by the taxonogenomics approach. The strain SN4^T was beige-colored, circular and not haemolytic. Cells are rod shaped and motile with several flagella. Strain SN4^T grows optimally at pH 7 and can survive in the presence of a saline concentration of up to 75 g/l NaCl. The 16S ribosomal RNA gene sequence analysis of the novel strain SN4^T showed 95.28% similarity in nucleotide sequence with Gorillibacterium massiliense G5^T, the phylogenetically closest neighbor and the type species of this genus. Anteiso-C_15:0, iso-C_15:0 and C_16:0 were found as the major components in the cellular fatty acid analysis of this isolate. The genomic draft of strain SN4^T is 5,263,742 bp long with 53.33% of G+C content. The differences in physiological, biochemical characteristics and phylogenetic and genomic data make it possible to clearly distinguish the strain SN4^T from G. massiliense G5^T. Based on the taxonogenomic description and the phenotypic and biochemical characteristics of this bacterium presented in this article, we propose the SN4^T strain (= CSUR P2011 = DSM 100,698) as a new species, Gorillibacterium timonense sp. nov.

Occurrence of Blastocystis-subtypes in patients from Italy revealed association of ST3 with a healthy gut microbiota

An epidemiological survey on Blastocystis was carried out enrolling a total of 2524 subjects referred to the Umberto I Academic Hospital in Rome, for the routine parasitological exams, during 2017–2018. The studied population included a sample of immunocompromised individuals (N = 130) followed at the same hospital.

DNA sequencing of the small subunit rRNA gene (SSU rDNA) locus was performed on samples positive to the coproparasitological analysis to molecular characterize the Blastocystis-subtypes.

Microscopical analysis detected Blastocystis in 192/2524 (7.6%) of the enrolled subjects. It was the organism most frequently identified in the analysed faecal samples diagnosed in single infection (5.6%) or in co-infection with other enteric protozoa (2%). Furthermore, it was found mainly in immunocompromised patients (22.3%) compared to immunocompetent ones (6.8%).

As expected, ST3 was the most occurring subtype identified in 40% of the subjects, followed by ST1 (29%), ST2 (16%), ST4 (12%), and ST7 (3%).

Next-generation sequencing (NGS) of the 16S rDNA was performed on a sub-sample of Blastocystis-ST3-carriers, homogenous by age and gender, as well as on Blastocystis-free subjects, to profile and compare their gut bacterial composition. A higher bacterial diversity was found in ST3-Blastocystis-carriers, which exhibited a high abundance of Prevotella, Methanobrevibacter and Ruminococcus while, a high percentage of Bacteroides was found in Blastocystis-free subjects.

This study evidenced the presence of Blastocystis in 7.6% of faecal samples in Italy and a high circulation of the protist among immunocompromised patients (22.3%). Molecular characterization of positive samples evidenced the occurrence of five different subtypes, including zoonotic ST such as the ST7, highlighting the risk of transmission from animals. Study of the gut microbiota composition confirms previous evidences according to which, the colonisation by Blastocystis would be linked with an eubiotic gut characterized by potentially beneficial species such as Prevotella and Ruminococcus, rather than with a dysbiotic state, with a high abundance of Enterobacteriaceae, and corroborated the role of the protist as “an old friend” of the human gut.

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Microscopical analysis detected Blastocystis in 7.6% subjects in Italy.

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Molecular methods allowed the identification of 5 STs (ST1, ST2, ST3, ST4, ST7).

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ST3 resulted the most frequent subtype.

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NGS of the 16S rDNA gene was performed in Blastocystis-ST3-carriers.

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Blastocystis-ST3 resulted correlated to an eubiotic gut characterized by potentially beneficial species.

Application of LpxC enzyme inhibitor to inhibit some fast-growing bacteria in human gut bacterial culturomics

BACKGROUND

Culturomics can ascertain traces of microorganisms to be cultivated using different strategies and identified by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry or 16S rDNA sequencing. However, to cater to all requirements of microorganisms and isolate as many species as possible, multiple culture conditions must be used, imposing a heavy workload. In addition, the fast-growing bacteria (e.g., Escherichia) surpass the slow-growing bacteria in culture by occupying space and using up nutrients. Besides, some bacteria (e.g., Pseudomonas) suppress others by secreting antibacterial metabolites, making it difficult to isolate bacteria with lower competence. Applying inhibitors to restrain fast-growing bacteria is one method to cultivate more bacterial species from human feces.

RESULTS

We applied CHIR-090, an LpxC enzyme inhibitor that has antibacterial activity against most Gram-negative bacteria, to culturomics of human fresh feces. The antibacterial activity of CHIR-090 was first assessed on five Gram-negative species of bacteria (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Proteus vulgaris, and Bacteroides vulgatus), all of which are commonly isolated from the human gut. Then, we assessed suitable concentrations of the inhibitor. Finally, CHIR-090 was applied in blood culture bottles for bacterial cultivation. In total, 102 species from five samples were identified. Of these, we found one new species, two species not reported previously in the human gut, and 11 species not previously isolated from humans.

CONCLUSIONS

CHIR-090 can suppress E. coli, P. aeruginosa, K. pneumoniae, Pro. vulgaris, but not B. vulgatus. Compared with the non-inhibitor group, CHIR-090 increased bacteria isolation by 23.50%, including four species not reported in humans and one new species. Application of LpxC enzyme inhibitor in culturomics increased the number of species isolated from the human gut.

Applying indirect open-circuit calorimetry to study energy expenditure in gnotobiotic mice harboring different human gut microbial communities

Given the increasing use of gnotobiotic mouse models for deciphering the effects of human microbial communities on host biology, there is a need to develop new methods for characterizing these animals while maintaining their isolation from environmental microbes. We describe a method for performing open-circuit indirect calorimetry on gnotobiotic mice colonized with gut microbial consortia obtained from different human donors. In this illustrative case, cultured collections of gut bacterial strains were obtained from obese and lean co-twins. The approach allows microbial contributions to host energy homeostasis to be characterized.

Cultivated Escherichia coli diversity in intestinal microbiota of Crohn's disease patients and healthy individuals: Whole genome data

Dysbiosis of the gut microbiota in inflammatory bowel disease (IBD) patients is of great interest. It has been reported that Crohn's disease (CD) is associated with a general decrease in microbial diversity [1]. Altered microbial composition and function in CD results in imbalance in host-bacteria interaction and increased immune stimulation [2]. It is shown that microbiota in CD is characterized by increased proportion of E. coli in human gut in contrast to healthy individuals [3]. However, the overall qualitative and quantitative diversity of E. coli strains in CD is not fully understood. Here, we present a dataset of whole-genome sequences of E. coli's.

Aging progression of human gut microbiota

Background

Human gut microbiota are important for human health and have been regarded as a “forgotten organ”, whose variation is closely linked with various factors, such as host genetics, diet, pathological conditions and external environment. The diversity of human gut microbiota has been correlated with aging, which was characterized by different abundance of bacteria in various age groups. In the literature, most of the previous studies of age-related gut microbiota changes focused on individual species in the gut community with supervised methods. Here, we aimed to examine the underlying aging progression of the human gut microbial community from an unsupervised perspective.

Results

We obtained raw 16S rRNA sequencing data of subjects ranging from newborns to centenarians from a previous study, and summarized the data into a relative abundance matrix of genera in all the samples. Without using the age information of samples, we applied an unsupervised algorithm to recapitulate the underlying aging progression of microbial community from hosts in different age groups and identify genera associated to this progression. Literature review of these identified genera indicated that for individuals with advanced ages, some beneficial genera are lost while some genera related with inflammation and cancer increase.

Conclusions

The multivariate unsupervised analysis here revealed the existence of a continuous aging progression of human gut microbiota along with the host aging process. The identified genera associated to this aging process are meaningful for designing probiotics to maintain the gut microbiota to resemble a young age, which hopefully will lead to positive impact on human health, especially for individuals in advanced age groups.

Serine protease inhibitors and human wellbeing interplay: new insights for old friends

Serine Protease Inhibitors (Serpins) control tightly regulated physiological processes and their dysfunction is associated to various diseases. Thus, increasing interest is given to these proteins as new therapeutic targets. Several studies provided functional and structural data about human serpins. By comparison, only little knowledge regarding bacterial serpins exists. Through the emergence of metagenomic studies, many bacterial serpins were identified from numerous ecological niches including the human gut microbiota. The origin, distribution and function of these proteins remain to be established. In this report, we shed light on the key role of human and bacterial serpins in health and disease. Moreover, we analyze their function, phylogeny and ecological distribution. This review highlights the potential use of bacterial serpins to set out new therapeutic approaches.

Cryopreservation of the human gut microbiota: Current state and perspectives

The human intestinal microbiota is a complex ecosystem that consists of thousands of bacterial species that are responsible for human health and disease. The intestinal microbiota is a natural resource for production of therapeutic and preventive medicals, such as probiotics and fecal transplants. Modern lifestyles have resulted in the extinction of evolutionally selected microbial populations upon exposure to environmental factors. Therefore, it is very important to preserve the human gut microbiota to have the opportunity for timely restoration with minimal safety risks. Cryopreservation techniques that are suitable for the preservation of viable, mixed microbial communities and a biobanking approach are currently under development in different countries. However, the number of studies in this area is very limited. The variety of morphological and physiological characteristics of microbes in the microbiota, the different cryopreservation goals, and the criteria for the evaluation of cryopreservation effectiveness are the main challenges in the creation of a universal and standardized cryopreservation protocol. In this review, we summarized the current progress of the main cryopreservation techniques for gut microbiota communities and the methods for the assessment of the effectiveness of these techniques in the context of practical application.

How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes

Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly of microbial communities.

Isolation of wheat bran-colonizing and metabolizing species from the human fecal microbiota

Undigestible, insoluble food particles, such as wheat bran, are important dietary constituents that serve as a fermentation substrate for the human gut microbiota. The first step in wheat bran fermentation involves the poorly studied solubilization of fibers from the complex insoluble wheat bran structure. Attachment of bacteria has been suggested to promote the efficient hydrolysis of insoluble substrates, but the mechanisms and drivers of this microbial attachment and colonization, as well as subsequent fermentation remain to be elucidated. We have previously shown that an individually dependent subset of gut bacteria is able to colonize the wheat bran residue. Here, we isolated these bran-attached microorganisms, which can then be used to gain mechanistic insights in future pure culture experiments. Four healthy fecal donors were screened to account for inter-individual differences in gut microbiota composition. A combination of a direct plating and enrichment method resulted in the isolation of a phylogenetically diverse set of species, belonging to the Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria phyla. A comparison with 16S rRNA gene sequences that were found enriched on wheat bran particles in previous studies, however, showed that the isolates do not yet cover the entire diversity of wheat-bran colonizing species, comprising among others a broad range of Prevotella, Bacteroides and Clostridium cluster XIVa species. We, therefore, suggest several modifications to the experiment set-up to further expand the array of isolated species.

Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa

Background

Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood.

Results

In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms.

Conclusions

Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165^T = DSM 17677^T = JCM 31915^T) and F. moorei sp. nov. (type strain ATCC 27768^T = NCIMB 13872^T).

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5313-6) contains supplementary material, which is available to authorized users.

Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in human gut

Background

The importance of the gut microbiota at the early stage of life and their longitudinal effect on host health have recently been well investigated. In particular, Bifidobacterium longum subsp. longum, a common component of infant gut microbiota, appears in the gut shortly after birth and can be detected there throughout an individual’s lifespan. However, it remains unclear whether this species colonizes in the gut over the long term from early infancy. Here, we investigated the long-term colonization of B. longum subsp. longum by comparing the genotypes of isolates obtained at different time points from individual subjects. Strains were isolated over time from the feces of 12 subjects followed from early infancy (the first six months of life) up to childhood (approximately six years of age). We also considered whether the strains were transmitted from their mothers’ perinatal samples (prenatal feces and postnatal breast milk).

Results

Intra-species diversity of B. longum subsp. longum was observed in some subjects’ fecal samples collected in early infancy and childhood, as well as in the prenatal fecal samples of their mothers. Among the highlighted strains, several were confirmed to colonize and persist in single individuals from as early as 90 days of age for more than six years; these were classified as long-term colonizers. One of the long-term colonizers was also detected from the corresponding mother’s postnatal breast milk. Quantitative polymerase chain reaction data suggested that these long-term colonizers persisted in the subjects’ gut despite the existence of the other predominant species of Bifidobacterium.

Conclusions

Our results showed that several strains belonging to B. longum subsp. longum colonized in the human gut from early infancy through more than six years, confirming the existence of long-term colonizers from this period. Moreover, the results suggested that these strains persisted in the subjects’ gut while co-existing with the other predominant bifidobacterial species. Our findings also suggested the importance of microbial-strain colonization in early infancy relative to their succession and showed the possibility that probiotics targeting infants might have longitudinal effects.

Trial Registration

TRN: ISRCTN25216339. Date of registration: 11/03/2016. Prospectively registered.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1358-6) contains supplementary material, which is available to authorized users.

Full-length title: NRPPUR database search and in vitro analysis identify an NRPS-PKS biosynthetic gene cluster with a potential antibiotic effect

Background

Growing concern about the emergence of antibiotic resistance is compelling the pharmaceutical industry to search for new antimicrobial agents. The availability of genome sequences has enabled the development of computational mining as an important tool in the discovery of natural products with antibiotic effect.

Results

NRPPUR (Non-Ribosomal Peptide and Polyketide Urmite) is a new bioinformatic tool that was created to detect polyketides and non-ribosomal peptide gene clusters (PKS and NRPS) in bacterial genomes using the rpsBlast program. The NRPPUR database was constructed locally by assembling all 3505 available sequences of NRPS-PKS that have been identified by in silico approaches to date, with 164 Biosynthetic Gene Clusters (BGCs) derived from the published literature that have demonstrated antimicrobial activity in vitro. The in silico analysis of 49 intestinal human bacterial genomes using the NRPPUR made it possible to identify 91 BGCs including 89 clusters that had never previously been described. On average, intestinal human bacterial genomes devote nearly 0.8% (±1.4% s.d.) of their genome to NRPS/PKS biosynthesis, with Bacillus vallismortis, Streptomyces massiliensis and Bacillus subtilis genomes apportioning 8.4, 3.6 and 3.15% of their genomes, respectively. When using the cross-streak method, S. massiliensis displayed antibacterial activity against many Gram-positive and negative bacteria including methicillin-resistant Staphylococcus aureus (MRSA).

Conclusions

NRPPUR has proven to be a very useful tool for the primary in silico selection of species with potential antimicrobial activity and human microbiota could be the future source of new antimicrobial discoveries. Further exploration of this and other ecological niches, coupled with high-throughput antibacterial activity screening should be envisaged.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2479-5) contains supplementary material, which is available to authorized users.