Acidaminococcus intestini sp. nov., isolated from human clinical samples

Examining the complex Interplay between gut microbiota abundance and short-chain fatty acid production in amyotrophic lateral sclerosis patients shortly after onset of disease

This study aimed to assess differences in the enteral microbiome of relatively recent-onset amyotrophic lateral sclerosis (ALS) patients (< 6-15 months since symptom onset) compared to healthy individuals, focusing on short-chain fatty acids (SCFAs) as potential mediators of host metabolism. We included 28 volunteers (16 ALS, 12 controls) with informed consent. No significant effect of ALS on alpha diversity (measuring the variety and abundance of species within a single sample, and indicating the health and complexity of the microbiome) was observed, but ALS patients had higher abundances of Fusobacteria and Acidobacteria. ALS subtypes influenced specific species, with increased Fusobacteria and Tenericutes in spinal ALS compared to bulbar ALS. ALS patients showed increased Enterobacter, Clostridium, Veillonella, Dialister, Turicibacter, and Acidaminococcus species and decreased Prevotella, Lactobacillus, and Butyricimonas. Correlations between species varied between ALS patients and healthy individuals and among ALS subtypes. No significant differences in SCFA concentrations were found, but spinal ALS samples showed a trend towards decreased propionate content. Relationships between SCFAs and phyla colonization differed by disease status. This study suggests distinct enteral microbiome characteristics in ALS patients, though the implications are unclear. Further research is needed to determine if these differences are causative or consequential and to explore their potential as diagnostic or therapeutic targets. The study also underscores the heterogeneity of microbiome constraints in ALS and the need for more research into ALS and SCFA metabolism.

Nitrate promotes the growth and the production of short-chain fatty acids and tryptophan from commensal anaerobe Veillonella dispar in the lactate-deficient environment by facilitating the catabolism of glutamate and aspartate

Veillonella spp. are nitrate-reducing bacteria with anaerobic respiratory activity that reduce nitrate to nitrite. They are obligate anaerobic, Gram-negative cocci that ferment lactate as the main carbon source and produce short-chain fatty acids (SCFAs). Commensal Veillonella reside in the human body site where lactate level is, however, limited for Veillonella growth. In this study, nitrate was shown to promote the anaerobic growth of Veillonella in the lactate-deficient media. We aimed to investigate the underlying mechanisms and the metabolism involved in nitrate respiration. Nitrate (15 mM) was demonstrated to promote Veillonella dispar growth and viability in the tryptone-yeast extract medium containing 0.5 mM L-lactate. Metabolite and transcriptomic analyses revealed nitrate enabled V. dispar to actively utilize glutamate and aspartate from the medium and secrete tryptophan. Glutamate or aspartate was further supplemented to a medium to investigate individual catabolism during nitrate respiration. Notably, nitrate was demonstrated to elevate SCFA production in the glutamate-supplemented medium, and further increase tryptophan production in the aspartate-supplemented medium. We proposed that the increased consumption of glutamate provided reducing power for nitrate respiration and aspartate served as a substrate for fumarate formation. Both glutamate and aspartate were incorporated into the central metabolic pathways via reverse tricarboxylic acid cycle and were linked with the increased production of acetate, propionate, and tryptophan. This study provides further understanding of the promoted growth and metabolic mechanisms by commensal V. dispar utilizing nitrate and specific amino acids to adapt to the lactate-deficient environment.IMPORTANCENitrate is a pivotal ecological factor influencing microbial community and metabolism. Dietary nitrate provides health benefits including anti-diabetic and anti-hypertensive effects via microbial-derived metabolites such as nitrite. Unraveling the impacts of nitrate on the growth and metabolism of human commensal bacteria is imperative to comprehend the intricate roles of nitrate in regulating microbial metabolism, community, and human health. Veillonella are lactate-utilizing, nitrate-reducing bacteria that are frequently found in the human body site where lactate levels are low and nitrate is at millimolar levels. Here, we comprehensively described the metabolic strategies employed by V. dispar to thrive in the lactate-deficient environment using nitrate respiration and catabolism of specific amino acids. The elevated production of SCFAs and tryptophan from amino acids during nitrate respiration of V. dispar further suggested the potential roles of nitrate and Veillonella in the promotion of human health.

Epilactose as a Promising Butyrate-Promoter Prebiotic via Microbiota Modulation

Epilactose is a disaccharide composed of galactose and mannose, and it is currently considered an "under development" prebiotic. In this study, we described the prebiotic potential of epilactose by in vitro fermentation using human fecal inocula from individuals following a Mediterranean diet (DM) or a Vegan diet (DV). The prebiotic effect of epilactose was also compared with lactulose and raffinose, and interesting correlations were established between metabolites and microbiota modulation. The production of several metabolites (lactate, short-chain fatty acids, and gases) confirmed the prebiotic properties of epilactose. For both donors, the microbiota analysis showed that epilactose significantly stimulated the butyrate-producing bacteria, suggesting that its prebiotic effect could be independent of the donor diet. Butyrate is one of the current golden metabolites due to its benefits for the gut and systemic health. In the presence of epilactose, the production of butyrate was 70- and 63-fold higher for the DM donor, when compared to lactulose and raffinose, respectively. For the DV donor, an increase of 29- and 89-fold in the butyrate production was obtained when compared to lactulose and raffinose, respectively. In conclusion, this study suggests that epilactose holds potential functional properties for human health, especially towards the modulation of butyrate-producing strains.

Associations between the rumen microbiota and carcass merit and meat quality in beef cattle

The rumen microbiota is important for energy and nutrient acquisition in cattle, and therefore its composition may also affect carcass merit and meat quality attributes. In this study, we examined the associations between archaeal and bacterial taxa in the rumen microbiota of beef cattle and 12 different attributes, including hot carcass weight (HCW), dressing percentage, ribeye area (REA), intramuscular fat content, marbling score, fat thickness, yield grade, moisture content, purge loss, and shear force. There were significant correlations between the relative abundance of certain archaeal and bacterial genera and these attributes. Notably, Selenomonas spp. were positively correlated with live weight and HCW, while also being negatively correlated with purge loss. Members of the Christensenellaceae R-7, Moryella, and Prevotella genera exhibited positive and significant correlations with various attributes, such as dressing percentage and intramuscular fat content. Ruminococcaceae UCG-001 was negatively correlated with live weight, HCW, and dressing percentage, while Acidaminococcus and Succinivibrionaceae UCG-001 were negatively correlated with intramuscular fat content, moisture content, and marbling score. Overall, our findings suggest that specific changes in the rumen microbiota could be a valuable tool to improve beef carcass merit and meat quality attributes. Additional research is required to better understand the relationship between the rumen microbiota and these attributes, with the potential to develop microbiome-targeted strategies for enhancing beef production. KEY POINTS: • Certain rumen bacteria were associated with carcass merit and meat quality • Moryella was positively correlated with intramuscular fat in beef carcasses • Acidaminococcus spp. was negatively correlated with marbling and intramuscular fat.

A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate

Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.

Water Quality, Toxicity and Diversity of Planktonic and Benthic Cyanobacteria in Pristine Ancient Lake Khubsugul (Hövsgöl), Mongolia

For the first time, microcystin-producing cyanobacteria have been detected in Khubsugul, which is ancient, pristine and one of the world’s largest lakes. The microcystin synthetase genes belonged to the genera Nostoc, Microcystis and possibly Snowella spp. No microcystins were found in the water of the lake. Using the HPLC-HRMS/TOF, five microcystin congeners were identified in biofilms from stony substrates sampled in the coastal zone. The concentration of microcystins in biofilms was low: 41.95 µg g−1 d. wt. by ELISA and 55.8 µg g−1 d. wt. using HPLC. The taxonomic composition of planktonic and benthic cyanobacterial communities was determined by means of microscopy and high-throughput sequencing of 16S rDNA amplicons. Nostocales cyanobacteria dominated benthos of Lake Khubsugul and Synechococcales—plankton. The abundance of cyanobacteria was low both in plankton and benthos; there was no mass development of cyanobacteria. Hydrochemical and microbiological analyses showed that the water in the lake was clean; the number of faecal microorganisms was significantly below the acceptable guideline values. Hydrochemical and hydrophysical parameters, and the concentration of chlorophyll a, were low and within the range of values recorded in the 1970s to 1990s, and corresponded to the oligotrophic state of the lake. There were no signs of anthropogenic eutrophication of the lake and no conditions for the cyanobacterial blooms.

Acidaminococcus homini s sp. nov., Amedibacillus hominis sp. nov., Lientehia hominis gen. nov. sp. nov., Merdimmobilis hominis gen. nov. sp. nov., and Paraeggerthella hominis sp. nov., isolated from human faeces

The human gastrointestinal tract is inhabited by various microorganisms, including thousands of bacterial taxa that have yet to be cultured and characterized. In this report, we describe the isolation, cultivation, genotypic and phenotypic characterization and taxonomy of five novel anaerobic bacterial strains that were recovered during the massive cultivation and isolation of gut microbes from human faecal samples. On the basis of the polyphasic taxonomic results, we propose two novel genera and five novel species. They are Acidaminococcus hominis sp. nov. (type strain NSJ-142^T=CGMCC 1.17903^T=KCTC 25346^T), Amedibacillus hominis sp. nov. (type strain NSJ-176^T=CGMCC 1.17933^T=KCTC 25355^T), Lientehia hominis gen. nov. sp. nov. (type strain NSJ-141^T=CGMCC 1.17902^T=KCTC 25345^T), Merdimmobilis hominis gen. nov. sp. nov. (type strain NSJ-153^T=CGMCC 1.17915^T=KCTC 25350^T) and Paraeggerthella hominis sp. nov. (type strain NSJ-152^T=CGMCC 1.17914^T=KCTC 25349^T).

Dietary Modulation of the Human Gut Microbiota and Metabolome with Flaxseed Preparations

Flaxseeds are typically consumed either as whole flaxseed, ground flaxseed, flaxseed oil, partially defatted flaxseed meal, or as a milk alternative. They are considered a rich source of vitamins, minerals, proteins and peptides, lipids, carbohydrates, lignans, and dietary fiber, which have shown hypolipidemic, antiatherogenic, anticholesterolemic, and anti-inflammatory property activity. Here, an in vitro batch culture model was used to investigate the influence of whole milled flaxseed and partially defatted milled flaxseed press cake on the gut microbiota and the liberation of flaxseed bioactives. Microbial communities were profiled using 16S rRNA gene-based high-throughput sequencing with targeted mass spectrometry measuring lignan, cyclolinopeptide, and bile acid content and HPLC for short-chain fatty acid profiles. Flaxseed supplementation decreased gut microbiota richness with Firmicutes, Proteobacteria, and Bacteroidetes becoming the predominant phyla. Secoisolariciresinol, enterodiol, and enterolactone were rapidly produced with acetic acid, butyric acid, and propionic acid being the predominant acids after 24 h of fermentation. The flaxseed press cake and whole flaxseed were equivalent in microbiota changes and functionality. However, press cake may be superior as a functional additive in a variety of foods in terms of consumer acceptance as it would be more resistant to oxidative changes.

Electricity production and key exoelectrogens in a mixed-culture psychrophilic microbial fuel cell at 4 °C

The electricity production via psychrophilic microbial fuel cell (PMFC) for wastewater treatment in cold regions offers an alternative to avoid the unwanted methane dissolution of traditional anaerobic fermentation. But, it is seldom reported by mixed-culture, especially closed to 0 °C. Thus, a two-chamber mixed-culture PMFC at 4 °C was successfully operated in this study using acetate as an electron donor. The main results demonstrated a good performance of PMFC, including the maximum voltage of 513 mV at 1000 Ω, coulombic efficiency of 53%, and power density of 689 mW/m². The cyclic voltammetry curves of enriched biofilm showed a direct electron transfer pathway. These good performances of mixed-culture PMFC were due to the high psychrophilic activity of enriched biofilm, including exoelectrogens genera of Geobacter (6.1%), Enterococcus (17.5%), and Clostridium_sensu_stricto_12 (3.8%). Consequently, a mixed-culture PMFC provides a reasonable strategy to enrich exoelectrogens with high activity. For low-temperature regions, the mixed-culture PMFC involved biotechnologies shall benefit energy generation and valuable chemical production in the future. KEY POINTS: • PMFC showed a maximum voltage of around 513 mV under a resistance of 1000 Ω. • The coulombic efficiency was 53% and the max power density was 689 mW/m². • Geobacter, Enterococcus, and Clostridium_sensu_stricto_12 were key exoelectrogens.

Use of 6 Nucleotide Length Words to Study the Complexity of Gene Sequences from Different Organisms

In this paper, we attempted to find a relation between bacteria living conditions and their genome algorithmic complexity. We developed a probabilistic mathematical method for the evaluation of k-words (6 bases length) occurrence irregularity in bacterial gene coding sequences. For this, the coding sequences from different bacterial genomes were analyzed and as an index of k-words occurrence irregularity, we used W, which has a distribution similar to normal. The research results for bacterial genomes show that they can be divided into two uneven groups. First, the smaller one has W in the interval from 170 to 475, while for the second it is from 475 to 875. Plants, metazoan and virus genomes also have W in the same interval as the first bacterial group. We suggested that second bacterial group coding sequences are much less susceptible to evolutionary changes than the first group ones. It is also discussed to use the W index as a biological stress value.

Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs

Despite the substantial progress made in human gut culturomics, little is known about the culturability of the swine gut microbiota. In this study, we cultured swine gut microbiota using 53 bacterial cultivation methods with different medium and gas combinations from three pigs at four different growth stages. Both culture-dependent (CD; colony mixtures from each method) and culture-independent (CI; original fecal suspensions) samples were subjected to 16S rRNA gene amplicon sequencing. Increasing microbial diversities were observed in both CI and CD samples from successive growth stages. While a total of 378, 482, 565, and 555 bacterial amplicon sequence variants (ASVs) were observed in the CI samples, higher microbial diversities (415, 675, 808, and 823 observed ASVs) were detected using the CD methods at the lactation, nursery, growing, and finishing stages, respectively. We constructed reference culture maps showing the preferred cultivation conditions for specific bacterial taxa and examined the effects of culturing factors such as oxygen, medium, donor pig age, antibiotics, and blood culture preincubation on swine gut microbiota cultivation. We focused on a wide range of beneficial bacteria, chose 1,299 colonies based on the reference map, and Sanger sequenced their 16S rRNA genes. These isolates clustered into 148 different bacterial taxa covering 28 genera. We observed 11, 19, 33, and 25 pairs of cooccurring ASVs in both CD and CI samples at four successive growth stages. This study provides guidance in culturing the swine gut microbiota of interest, which is critical when characterizing their functions in this important animal species.

IMPORTANCE The swine gut microbiome has been the focus of many investigations due to the fact that pigs serve as both an excellent biomedical model for human diseases and an important protein source. Substantial progress has been made in swine gut microbiome studies using next-generation sequencing-based culture-independent approaches, but little is known about the culturability of the swine gut microbiota. To understand their roles in swine production, it is critical to culture bacterial strains of interest. In this study, we cultured the gut microbiota from pigs at different growth stages using 53 bacterial cultivation methods with different medium and gas combinations. This study provides evidence that the swine gut microbiota is much more diverse based on a culture-dependent approach than previously known. It provides preliminary guidance for isolating certain bacteria of interest from pigs, which is critical in establishing causal relationships between the gut microbiota and the health status of pigs.

Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy

Gut bacterial microbiome dysbiosis in type 2 Diabetes Mellitus (T2DM) has been reported, but such an association with Diabetic Retinopathy (DR) is not known. We explored possible link between gut bacterial microbiome dysbiosis and DR. Using fecal samples of healthy controls (HC) and people with T2DM with/without DR, gut bacterial communities were analysed using 16S rRNA gene sequencing and data analysed using QIIME and R software. Dysbiosis in the gut microbiomes, at phyla and genera level, was observed in people with T2DM and DR compared to HC. People with DR exhibited greater discrimination from HC. Microbiomes of people with T2DM and DR were also significantly different. Both DM and DR microbiomes showed a decrease in anti-inflammatory, probiotic and other bacteria that could be pathogenic, compared to HC, and the observed change was more pronounced in people with DR. This is the first report demonstrating dysbiosis in the gut microbiome (alteration in the diversity and abundance at the phyla and genera level) in people with DR compared to HC. Such studies would help in developing novel and targeted therapies to improve treatment of DR.

Dietary inflammatory potential in relation to the gut microbiome: results from a cross-sectional study

Diet has direct and indirect effects on health through inflammation and the gut microbiome. We investigated total dietary inflammatory potential via the literature-derived index (Dietary Inflammatory Index (DII®)) with gut microbiota diversity, composition and function. In cancer-free patient volunteers initially approached at colonoscopy and healthy volunteers recruited from the medical centre community, we assessed 16S ribosomal DNA in all subjects who provided dietary assessments and stool samples (n 101) and the gut metagenome in a subset of patients with residual fasting blood samples (n 34). Associations of energy-adjusted DII scores with microbial diversity and composition were examined using linear regression, permutational multivariate ANOVA and linear discriminant analysis. Spearman correlation was used to evaluate associations of species and pathways with DII and circulating inflammatory markers. Across DII levels, α- and β-diversity did not significantly differ; however, Ruminococcus torques, Eubacterium nodatum, Acidaminococcus intestini and Clostridium leptum were more abundant in the most pro-inflammatory diet group, while Akkermansia muciniphila was enriched in the most anti-inflammatory diet group. With adjustment for age and BMI, R. torques, E. nodatum and A. intestini remained significantly associated with a more pro-inflammatory diet. In the metagenomic and fasting blood subset, A. intestini was correlated with circulating plasminogen activator inhibitor-1, a pro-inflammatory marker (rho = 0·40), but no associations remained significant upon correction for multiple testing. An index reflecting overall inflammatory potential of the diet was associated with specific microbes, but not overall diversity of the gut microbiome in our study. Findings from this preliminary study warrant further research in larger samples and prospective cohorts.

Gut microbiota composition in children with obstructive sleep apnoea syndrome: a pilot study

BACKGROUND

Obstructive Sleep Apnoea syndrome (OSAS) is considered a systemic inflammatory disease and is characterized by intermittent hypoxia that can damage the integrity of intestinal barrier and alter gut microbiota composition in adults and animal models. To date there is only one study on snoring children and microbiota but no studies are present on paediatric OSAS related dysbiosis.

STUDY OBJECTIVES

To evaluate gut microbiota composition in OSAS children in respect to healthy subjects and investigate the role of sleep parameters in changing gut microbiome.

METHODS

Sixteen children divided in OSAS and healthy groups. Stool samples were collected from both the two groups to assess gut microbiota composition using 16S rRNA sequencing and a nocturnal pulsossimetry and polysomnography were performed in OSAS children.

RESULTS

OSAS children showed a decreased microbial diversity in respect to healthy subjects in terms of number of observed species and Chao1 index (p = 0,01). Firmicutes/Bacteroidetes ratio was directly correlated to Sleep Clinical Record (p = 0,03). The abundance of several inflammation-related strains (Proteobacteria, Clostridiaceae, Oscillospiraceae, Klebsiella) were found significantly modified in relation to sleep parameters. Bacteria implied in the gut barrier integrity (Desulfovibrionaceae, Bacteroides fragilis and Faecalibacterium prausnitzii) were found significantly different in the two study groups and correlated with sleep parameters.

CONCLUSIONS

OSAS children showed a lower microbiota diversity in respect to heathy subjects and an increase of inflammation and gut barrier disruptors-related strains probably induced by intermittent hypoxia. Further studies should be conducted to understand the role of gut microbiota in OSAS physiopathology and comorbidities in children.

Exopolysaccharides From Lactobacillus paracasei Isolated From Kefir as Potential Bioactive Compounds for Microbiota Modulation

Microbiota coexists in true symbiosis with the host playing pivotal roles as a key element for well-being and health. Exopolysaccharides from lactic acid bacteria are an alternative as novel potential prebiotics that increase microbiota diversity. Considering this, the aim of the present work was to evaluate the capacity of the EPS produced by two L. paracasei strains isolated from kefir grains, to be metabolized in vitro by fecal microbiota producing short chain fatty acids. For this purpose, fecal samples from healthy children were inoculated in a basal medium with EPS and incubated in anaerobiosis at 37°C for 24, 48, and 72 h. DGGE profiles and the production of SCFA after fermentation were analyzed. Additionally, three selected samples were sequenced by mass sequencing analysis using Ion Torrent PGM. EPS produced by L. paracasei CIDCA 8339 (EPS₈₃₃₉) and CIDCA 83124 (EPS₈₃₁₂₄) are metabolized by fecal microbiota producing a significant increase in SCFA. EPS₈₃₃₉ fermentation led to an increment of propionate and butyrate, while fermentation of EPS₈₃₁₂₄ increased butyrate levels. Both EPS led to a profile of SCFA different from the ones obtained with inulin or glucose fermentation. DGGE profiles of 72 h fermentation demonstrated that both EPS showed a different band profile when compared to the controls; EPS profiles grouped in a cluster that have only 65% similarity with glucose or inulin profiles. Mass sequencing analysis demonstrated that the fermentation of EPS₈₃₃₉ leads to an increase in the proportion of the genera Victivallis, Acidaminococcus and Comamonas and a significant drop in the proportion of enterobacteria. In the same direction, the fermentation of EPS₈₃₁₂₄ also resulted in a marked reduction of Enterobacteriaceae with a significant increase in the genus Comamonas. It was observed that the changes in fecal microbiota and SCFA profile exerted by both polymers are different probably due to differences in their structural characteristics. It can be concluded that EPS synthesized by both L. paracasei strains, could be potentially used as bioactive compound that modify the microbiota increasing the production of propionic and butyric acid, two metabolites highly associated with beneficial effects both at the gastrointestinal and extra-intestinal level.

Multimodal Approach to Assessment of Fecal Microbiota Donors based on Three Complementary Methods

Methods of stool assessment are mostly focused on next-generation sequencing (NGS) or classical culturing, but only rarely both. We conducted a series of experiments using a multi-method approach to trace the stability of gut microbiota in various donors over time, to find the best method for the proper selection of fecal donors and to find "super-donor" indicators. Ten consecutive stools donated by each of three donors were used for the experiments (30 stools in total). The experiments assessed bacterial viability measured by flow cytometry, stool culturing on different media and in various conditions, and NGS (90 samples in total). There were no statistically significant differences between live and dead cell numbers; however, we found a group of cells classified as not-dead-not-alive, which may be possibly important in selection of "good" donors. Donor C, being a regular stool donor, was characterized by the largest number of cultivable species (64). Cultivable core microbiota (shared by all donors) was composed of only 16 species. ANCOM analysis of NGS data highlighted particular genera to be more abundant in one donor vs. the others. There was a correlation between the not-dead-not-alive group found in flow cytometry and Anaeroplasma found by NGS, and we could distinguish a regular stool donor from the others. In this work, we showed that combining various methods of microbiota assessment gives more information than each method separately.

Planktonic and Sessile Artificial Colonic Microbiota Harbor Distinct Composition and Reestablish Differently upon Frozen and Freeze-Dried Long-Term Storage

Fecal microbiota transplantation has been successfully applied in the treatment of recurrent Clostridium difficile infection and has been suggested as an alternative therapy for other intestinal disorders such as inflammatory bowel disease or metabolic syndrome. “Artificial” colonic microbiota delivered by PolyFermS continuous fermentation models can provide a controllable and reproducible alternative to fecal transplantation, but effective preservation strategies must be developed. In this study, we systematically investigated the response of sessile and planktonic artificial colonic microbiota to cryopreservation and lyophilization. We suggest that functional redundancy is an important factor in providing functional stability with respect to exposure to stress during processing and storage. Functional redundancy in compositionally reduced microbial systems may be considered when designing microbial products for therapy.

Biofilm-associated, sessile communities represent the major bacterial lifestyle, whereas planktonic cells mainly appear during initial colonization of new surfaces. Previous research, mainly performed with pathogens, demonstrated increased environmental stress tolerance of biofilm-growing compared to planktonic bacteria. The lifestyle-specific stress response of colonic microbiota, both natural and fermentation produced, has not been addressed before. Planktonic and sessile “artificial” colonic microbiota delivered by PolyFermS continuous fermentation models can provide a controllable and reproducible alternative to fecal transplantation in treating gastrointestinal disorders. We therefore characterized planktonic and sessile microbiota produced in two PolyFermS models inoculated with immobilized fecal microbiota and comparatively tested their levels of tolerance of frozen storage (–80°C) and freeze-dried storage (4°C) for 9 months to mimic preservation strategies for therapeutic applications. Sessile microbiota harbored next to shared taxa a unique community distinguishable from planktonic microbiota. Synergistetes and Proteobacteria were highly represented in sessile microbiota, while Firmicutes were more abundant in planktonic microbiota. The community structure and metabolic activity of both microbiota, monitored during standardized reactivation batch fermentations, were better preserved after frozen storage than dried storage, indicated by higher Bray-Curtis similarity and enhanced recovery of metabolite production. For both lifestyles, reestablishment of Bacteroidaceae was impaired after frozen and dried storage along with reduced propionate formation. In contrast, butyrate production was maintained after reactivation despite compositional rearrangements within the butyrate-producing community. Unexpectedly, the rate of recovery of metabolite production was lower after preservation of sessile than planktonic microbiota. We speculate that higher functional dependencies between microbes might have led to the lower stress tolerance of sessile than planktonic microbiota.

IMPORTANCE Fecal microbiota transplantation has been successfully applied in the treatment of recurrent Clostridium difficile infection and has been suggested as an alternative therapy for other intestinal disorders such as inflammatory bowel disease or metabolic syndrome. “Artificial” colonic microbiota delivered by PolyFermS continuous fermentation models can provide a controllable and reproducible alternative to fecal transplantation, but effective preservation strategies must be developed. In this study, we systematically investigated the response of sessile and planktonic artificial colonic microbiota to cryopreservation and lyophilization. We suggest that functional redundancy is an important factor in providing functional stability with respect to exposure to stress during processing and storage. Functional redundancy in compositionally reduced microbial systems may be considered when designing microbial products for therapy.

Primary progressive multiple sclerosis in a Russian cohort: relationship with gut bacterial diversity

Background

Gut microbiota has been increasingly acknowledged to shape significantly human health, contributing to various autoimmune diseases, both intestinal and non-intestinal, including multiple sclerosis (MS). Gut microbiota studies in patients with relapsing remitting MS strongly suggested its possible role in immunoregulation; however, the profile and potential of gut microbiota involvement in patients with primary progressive MS (PPMS) patients has received much less attention due to the rarity of this disease form. We compared the composition and structure of faecal bacterial assemblage using Illumina MiSeq sequencing of V3-V4 hypervariable region of 16S rRNA genes amplicons in patients with primary progressive MS and in the healthy controls.

Results

Over all samples 12 bacterial phyla were identified, containing 21 classes, 25 orders, 54 families, 174 genera and 1256 operational taxonomic units (OTUs). The Firmicutes phylum was found to be ultimately dominating both in OTUs richness (68% of the total bacterial OTU number) and in abundance (71% of the total number of sequence reads), followed by Bacteroidetes (12 and 16%, resp.) and Actinobacteria (7 and 6%, resp.). Summarily in all samples the number of dominant OTUs, i.e. OTUs with ≥1% relative abundance, was 13, representing much less taxonomic richness (three phyla, three classes, four orders, six families and twelve genera) as compared to the total list of identified OTUs and accounting for 30% of the sequence reads number in the healthy cohort and for 23% in the PPMS cohort. Human faecal bacterial diversity profiles were found to differ between PPMS and healthy cohorts at different taxonomic levels in minor or rare taxa. Marked PPMS-associated increase was found in the relative abundance of two dominant OTUs (Gemmiger sp. and an unclassified Ruminococcaceae). The MS-related differences were also found at the level of minor and rare OTUs (101 OTUs). These changes in OTUs’ abundance translated into increased bacterial assemblage diversity in patients.

Conclusion

The findings are important for constructing a more detailed global picture of the primary progressive MS-associated gut microbiota, contributing to better understanding of the disease pathogenesis.

Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition

Background

The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs.

Results

Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis.

Conclusions

The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1918-5) contains supplementary material, which is available to authorized users.

Gut microbiota in obstructive sleep apnea-hypopnea syndrome: disease-related dysbiosis and metabolic comorbidities

Gut microbiota alterations manifest as intermittent hypoxia and fragmented sleep, thereby mimicking obstructive sleep apnea–hypopnea syndrome (OSAHS). Here, we sought to perform the first direct survey of gut microbial dysbiosis over a range of apnea–hypopnea indices (AHI) among patients with OSAHS. We obtained fecal samples from 93 patients with OSAHS [5 < AHI ≤ 15 (n=40), 15 < AHI ≤ 30 (n=23), and AHI ≥ 30 (n=30)] and 20 controls (AHI ≤ 5) and determined the microbiome composition via 16S rRNA pyrosequencing and bioinformatics analysis of variable regions 3–4. We measured fasting levels of homocysteine (HCY), interleukin-6 (IL-6), and tumor necrosis factor α (TNF-α). Results revealed gut microbial dysbiosis in several patients with varying severities of OSAHS, reliably separating them from controls with a receiver operating characteristic-area under the curve (ROC-AUC) of 0.789. Functional analysis in the microbiomes of patients revealed alterations; additionally, decreased in short-chain fatty acid (SCFA)-producing bacteria and increased pathogens, accompanied by elevated levels of IL-6. Lactobacillus levels correlated with HCY levels. Stratification analysis revealed that the Ruminococcus enterotype posed the highest risk for patients with OSAHS. Our results show that the presence of an altered microbiome is associated with HCY among OSAHS patients. These changes in the levels of SCFA affect the levels of pathogens that play a pathophysiological role in OSAHS and related metabolic comorbidities.

Spoilage microbial community profiling by 16S rRNA amplicon sequencing of modified atmosphere packaged live mussels stored at 4oC

There is little information on the microbial communities associated with modified atmosphere (MA)-packaged live mussels. There is also a dearth of information on how pre-packaging depuration modifies the microbial communities and spoilage of live mussels. Amplicon sequencing was used to describe spoilage microbial succession in MA-packaged live mussels during storage at 4 °C. Proteobacteria, Cyanobacteria and Firmicutes were the three major phyla observed in the mussel meat and pouch water of undepurated and depurated mussels. Among these phyla, Cyanobacteria was more predominant on day 0 in mussel meat of undepurated and depurated mussels while Proteobacteria was predominant in commercially-depurated mussels. Synechococcus was apparently dominant on days 0-7 in the meat of undepurated mussels and days 0-10 in depurated mussels. Shewanella was dominant on day 0 in commercially-depurated mussels and dominant on day 15 in undepurated while Acidaminococcus was dominant in depurated mussels on day 15. Psychromonas was observed to be dominant in commercially-depurated mussels on day 7 and further shifted to Acinetobacter by day 10 and 15. In the pouch water, Acinetobacter was dominant throughout the storage days in undepurated mussels while Psychrobacter was predominant in both depurated and commercially-depurated mussels. This study demonstrated the impact of depuration on the microbiota and the spoilage mechanism of MA-packaged live mussels. Shewanella was easily removed through depuration. However, spoilage bacteria such as Acidaminococcus could not be easily removed although they are not important at the beginning but grew at the end. Pouch water contributed suitable biological medium for the growth of Acinetobacter and Psychrobacter and both enhanced the growth of spoilage bacteria such as Shewanella and Acidaminococcus.

Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels

Unabsorbed copper accumulates in the hindgut of pigs that consume high levels of dietary copper, which enhances the coselection of antibiotic-resistant bacteria and is considered detrimental to the environment and to porcine health. In our study, a combination of 16S rRNA pyrosequencing and nontargeted metabolomics was used to investigate the microbiome-metabolome responses to dietary copper levels in the hindgut of suckling piglets. The results showed that the dietary copper level affected the abundance of several Clostridia genera and that the relative abundance of butyrate-producing bacteria, such as Coprococcus, Roseburia, and Acidaminococcus, was reduced in the 300 mg kg⁻¹ (high) Cu group. Metabolomic analysis revealed that dietary copper levels affected protein and carbohydrate metabolites, protein biosynthesis, the urea cycle, galactose metabolism, gluconeogenesis, and amino acid metabolism (including the metabolism of arginine, proline, β-alanine, phenylalanine, tyrosine, and methionine). Furthermore, Pearson’s correlation analysis showed that the abundance levels of Coprococcus (family Lachnospiraceae) and operational taxonomic unit (OTU) 18 (family Ruminococcaceae) were positively correlated with energy metabolism pathways (gluconeogenesis, glycolysis, and the pentose phosphate pathway). The abundance of Streptococcus was negatively correlated with amino acid metabolism pathways (protein biosynthesis, glycine, serine, threonine, methionine, phenylalanine, and tyrosine metabolism), and OTU583 and OTU1067 (family Rikenellaceae) were positively correlated with amino acid metabolism pathways. These results suggest that the copper levels consumed by LC (low-copper group) versus HC (high-copper group) animals alter the composition of the gut microbiota and modulate microbial metabolic pathways, which may further affect the health of suckling piglets.

Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor

Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 day hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community. After stable operation was established in the bioreactor, the mixing intensity was increased in order to investigate the effect of a physical disruption of the microbial community structure. Finally, the original conditions were re-established to understand the stability of the microbial community after a perturbation. All factors measured were found to be inter-correlated during these three distinct phases of operation (establishment, perturbation and re-establishment). In particular, the return of community structure and function to pre-perturbed conditions suggests that propionate fermentation and acetate utilization were the explanatory factors for community establishment and re-establishment.

Alterations in the gut bacterial microbiome in fungal Keratitis patients

Dysbiosis in the gut microbiome has been implicated in several diseases including auto-immune diseases, inflammatory diseases, cancers and mental disorders. Keratitis is an inflammatory disease of the eye significantly contributing to corneal blindness in the developing world. It would be worthwhile to investigate the possibility of dysbiosis in the gut microbiome being associated with Keratitis. Here, we have analyzed fungal and bacterial populations in stool samples through high-throughput sequencing of the ITS2 region for fungi and V3-V4 region of 16S rRNA gene for bacteria in healthy controls (HC, n = 31) and patients with fungal keratitis (FK, n = 32). Candida albicans (2 OTUs), Aspergillus (1 OTU) and 3 other denovo-OTUs were enriched in FK samples and an unclassified denovo-OTU was enriched in HC samples. However, the overall abundances of these ‘discriminatory’ OTUs were very low (< 0.001%) and not indicative of significant dysbiosis in the fungal community inhabiting the gut of FK patients. In contrast, the gut bacterial richness and diversity in FK patients was significantly decreased when compared to HC. 52 OTUs were significantly enriched in HC samples whereas only 5 OTUs in FK. The OTUs prominently enriched in HC were identified as Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Lachnospira, Mitsuokella multacida, Bacteroides plebeius, Megasphaera and Lachnospiraceae. In FK samples, 5 OTUs affiliated to Bacteroides fragilis, Dorea, Treponema, Fusobacteriaceae, and Acidimicrobiales were significantly higher in abundance. The functional implications are that Faecalibacterium prausnitzii, an anti-inflammatory bacterium and Megasphaera, Mitsuokella multacida and Lachnospira are butyrate producers, which were enriched in HC patients, whereas Treponema and Bacteroides fragilis, which are pathogenic were abundant in FK patients, playing a potential pro-inflammatory role. Heatmap, PCoA plots and functional profiles further confirm the distinct patterns of gut bacterial composition in FK and HC samples. Our study demonstrates dysbiosis in the gut bacterial microbiomes of FK patients compared to HC. Further, based on inferred functions, it appears that dysbiosis in the gut of FK subjects is strongly associated with the disease phenotype with decrease in abundance of beneficial bacteria and increase in abundance of pro-inflammatory and pathogenic bacteria.

'Acidaminococcus timonensis' sp. nov. and 'Acidaminococcus massiliensis' sp. nov. isolated from human gut

We report here the main characteristics of 'Acidaminococcus timonensis' strain Marseille-P2764T, isolated from human right colon, and 'Acidaminococcus massiliensis' strain Marseille-P2828T, isolated from human duodenum.

Correlations between bacterial populations and process parameters in four full-scale anaerobic digesters treating sewage sludge

Process parameters and bacterial populations were investigated in four full-scale anaerobic digesters treating sewage sludge. Although the four digesters were operated under similar conditions, digesters A and B had higher pH (7.2-7.4) and lipid removal efficiencies (>50%) than C and D (pH 6.1-6.4; average lipid removal <16%). Bacterial richness, diversity, and evenness were higher in digesters C and D. Among the top-populated genera, ten (group I) were more abundant in digesters A and/or B; they were putative syntrophic fatty acid or protein/amino acid-utilizers. In contrast, fifteen others (group II) were less abundant in A and/or B and included potentially dormant/dead cells originated from activated sludge. Despite the overall richness trend, the presence of the 25 genera in groups I/II was greater in digesters A and B (24) than in C and D (17); this observation suggests that group I bacteria might be essential in AD of sewage sludge.

Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota

BACKGROUND

Chronic malnutrition, termed stunting, is defined as suboptimal linear growth, affects one third of children in developing countries, and leads to increased mortality and poor developmental outcomes. The causes of childhood stunting are unknown, and strategies to improve growth and related outcomes in children have only had modest impacts. Recent studies have shown that the ecosystem of microbes in the human gut, termed the microbiota, can induce changes in weight. However, the specific changes in the gut microbiota that contribute to growth remain unknown, and no studies have investigated the gut microbiota as a determinant of chronic malnutrition.

RESULTS

We performed secondary analyses of data from two well-characterized twin cohorts of children from Malawi and Bangladesh to identify bacterial genera associated with linear growth. In a case-control analysis, we used the graphical lasso to estimate covariance network models of gut microbial interactions from relative genus abundances and used network analysis methods to select genera associated with stunting severity. In longitudinal analyses, we determined associations between these selected microbes and linear growth using between-within twin regression models to adjust for confounding and introduce temporality. Reduced microbiota diversity and increased covariance network density were associated with stunting severity, while increased relative abundance of Acidaminococcus sp. was associated with future linear growth deficits.

CONCLUSIONS

We show that length growth in children is associated with community-wide changes in the gut microbiota and with the abundance of the bacterial genus, Acidaminococcus. Larger cohorts are needed to confirm these findings and to clarify the mechanisms involved.

Changes of the human gut microbiome induced by a fermented milk product

The gut microbiota (GM) consists of resident commensals and transient microbes conveyed by the diet but little is known about the role of the latter on GM homeostasis. Here we show, by a conjunction of quantitative metagenomics, in silico genome reconstruction and metabolic modeling, that consumption of a fermented milk product containing dairy starters and Bifidobacterium animalis potentiates colonic short chain fatty acids production and decreases abundance of a pathobiont Bilophila wadsworthia compared to a milk product in subjects with irritable bowel syndrome (IBS, n = 28). The GM changes parallel improvement of IBS state, suggesting a role of the fermented milk bacteria in gut homeostasis. Our data challenge the view that microbes ingested with food have little impact on the human GM functioning and rather provide support for beneficial health effects.

Changes of poultry faecal microbiota associated with Clostridium difficile colonisation

Bacterial, fungal and archaeal microbiota was analysed in 143 chicken faecal samples from a single poultry farm. After DHPLC (denaturing high performance liquid chromatography) 15 bacterial groups, 10 fungal groups and a single archaeal species were differentiated. Samples were grouped into two clusters with significantly different frequencies of C. difficile positive and negative samples in each cluster. Acidaminococcus intestini, described here for the first time as a part of poultry faecal microbiota, was significantly more likely present in C. difficile negative samples, while presence/absence of some other microorganisms (Enterococcus cecorum, Lactobacillus galinarum, Moniliella sp. and Trichosporon asahii) was close to significance. Two other groups not reported previously for poultry, Coprobacillus sp. and Turicibacter sp. did not differ significantly between C. difficile positive and negative samples. Differences in microbiota diversity depend on animal age, but not on the presence of C. difficile. With machine learning (WEKA J48) we have defined specific combinations of microbial groups predictive for C. difficile colonisation. Microbial groups associated with C. difficile colonisation in poultry are different than those reported for humans and include bacteria as well as fungi. Also with this approach A. intestini was found to be most strongly related to C. difficile negative samples.

Complete genome sequence of Acidaminococcus intestini RYC-MR95, a Gram-negative bacterium from the phylum Firmicutes

Acidaminococcus intestini belongs to the family Acidaminococcaceae, order Selenomonadales, class Negativicutes, phylum Firmicutes. Negativicutes show the double-membrane system of Gram-negative bacteria, although their chromosomal backbone is closely related to that of Gram-positive bacteria of the phylum Firmicutes. The complete genome of a clinical A. intestini strain is here presented.

Complete genome sequence of Acidaminococcus fermentans type strain (VR4)

Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococcus, and is of phylogenetic interest because of its isolated placement in a genomically little characterized region of the Firmicutes. A. fermentans is known for its habitation of the gastrointestinal tract and its ability to oxidize trans-aconitate. Its anaerobic fermentation of glutamate has been intensively studied and will now be complemented by the genomic basis. The strain described in this report is a nonsporulating, nonmotile, Gram-negative coccus, originally isolated from a pig alimentary tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Acidaminococcaceae, and the 2,329,769 bp long genome with its 2,101 protein-coding and 81 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their dnaK gene sequences. The isolates were affiliated to the family Veillonellaceae, the coccobacillus Dialister micraerophilus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family Veillonellaceae. A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus Negativicoccus gen. nov., with the novel species Negativicoccus succinicivorans sp. nov. [type strain ADV 07/08/06-B-1388(T) (=AIP 149.07(T)=CIP 109806(T)=DSM 21255(T)=CCUG 56017(T)) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum Firmicutes and other phyla indicated that the family Veillonellaceae forms a robust lineage clearly separated from those of the classes 'Bacilli', 'Clostridia', Thermolithobacteria and 'Erysipelotrichi' in the phylum Firmicutes. Therefore, we propose that this family is a class-level taxon in the phylum Firmicutes, for which the name Negativicutes classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order Selenomonadales ord. nov. In this order, a novel family, Acidaminococcaceae fam. nov., is proposed and description of the family Veillonellaceae is emended.

[New anaerobic bacterial species in human infections]

This review offers succinct, precise, and complete information based on the available data concerning new anaerobic bacterial species involved in infectious diseases in humans. All hitherto undescribed species, those not previously implicated in clinical conditions, those with confirmed implication in human disease that have not been characterized, and those that have undergone taxonomic changes are considered to be "new".