Biology subjects

Blohs, M.

Publications and source records attributed to Blohs, M..

6 recordsLinked to original sources

bioRxiv2024

Expanding the cultivable human archaeome: Methanobrevibacter intestini sp. nov. and strain Methanobrevibacter smithii GRAZ-2 from human feces

Two mesophilic, hydrogenotrophic methanogens, WWM1085 and M. smithii GRAZ-2 were isolated from human fecal samples. WWM1085 was isolated from an individual in the USA, and represents a novel species with in the genus Methanobrevibacter. M. smithii GRAZ-2 (= DSM 116045) was retrieved from fecal samples of a European, healthy female and represents a novel strain within this genus. Both Methanobrevibacter representatives form non-flagellated, short rods with variable morphologies and the capacity to form filaments. Both isolates showed the typical fluorescence of F420 and methane production. Compared to M. smithii GRAZ-2, WWM1085 did not accumulate formate when grown on H2 and CO2. The optimal growth conditions were at 37{degrees}C, and pH 7. Full genome sequencing revealed a genomic difference of WWM1085 to the type strain of M. smithii PS (type strain; DSM 861), with 93.55% ANI and major differences in the sequence of its mcrA gene (3.3% difference in nucleotide sequence). Differences in the 16S rRNA gene were very minor and thus distinction based on this sequence might not be possible. M. smithii GRAZ-2 was identified as a novel strain within the Methanobrevibacter genus (ANI 99.04 % to M. smithii PS). Due to the major differences of WWM1085 and M. smithii type strain PS in phenotypic, genomic and metabolic features, we propose M. intestini sp. nov. as a novel species with WWM1085 as the type strain (DSM 116060T = CECT 30992).

microbiology↗

bioRxiv2024

Expanding the cultivated human archaeome by targeted isolation of novel Methanobrevibacter strains from fecal samples

Archaea are integral components of the human microbiome but persist as understudied entities within the gastrointestinal tract (GIT), primarily due to the lack of cultured representatives for comprehensive mechanistic investigations. With only four Methanobrevibacter smithii isolates from humans available according to the Global Catalogue of Microorganisms (GCM), the existing cultures fail to adequately represent the observed diversity, as underscored by recent findings. This study introduces a targeted cultivation method for enriching methanogenic archaea from human fecal samples. Applied to 16 stool samples from healthy and diseased donors, the method aimed to genomically characterize the archaeal cultures and establish correlations with gastrointestinal disorders. The procedure combines methane breath testing, in silico metabolic modelling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyses include co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which were absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from diverse participant cohorts revealed features potentially associated with gastrointestinal diseases. This work substantially broadens the scope of available archaeal representatives for functional and mechanistic studies in the human GIT. The established protocol facilitates the cultivation of methanogenic archaea from nearly every human fecal sample, offering insights into the adaptability of Candidatus Methanobrevibacter intestini genomes in critical microbiome situations.

microbiology↗

bioRxiv2022

The origin of floral quartet formation - Ancient exon duplications shaped the evolution of MIKC-type MADS-domain transcription factor interactions

During development of flowering plants, some MIKC-type MADS-domain transcription factors (MTFs) exert their regulatory function as heterotetrameric complexes bound to two sites on the DNA of target genes. This way they constitute "floral quartets" or related "floral quartet-like complexes" (FQCs), involving a unique multimeric system of paralogous protein interactions. Tetramerisation of MTFs is brought about mainly by interactions of keratin-like (K) domains. The K-domain associated with the more ancient DNA-binding MADS-domain during evolution in the stem group of extant streptophytes (charophyte green algae + land plants). However, whether this was sufficient for MTF tetramerisation and FQC formation to occur, remains unknown. Here, we provide biophysical and bioinformatic data indicating that the ancestral MTFs were not able to form FQCs. According to our data, FQC formation originated in the stem group of land plants in a sublineage of MIKC-type genes termed MIKCC-type genes. In the stem group of this gene lineage, the duplication of the most downstream exon encoding the K-domain led to a C-terminal elongation of the second K-domain helix, thus generating the tetramerisation interface found in extant MIKCC-type proteins. In the stem group of the sister lineage of the MIKCC-type genes, termed MIKC*-type genes, the duplication of two other exons of the K-domain occurred, extending the K-domain at its N-terminal end. Our data indicate that this structural change prevents heterodimerisation between MIKCC-type and MIKC*-type proteins. This way, two largely independent gene regulatory networks could be established, featuring MIKCC-type or MIKC*-type proteins, respectively, that control different aspects of plant development.

genetics↗

bioRxiv2022

Acute appendicitis manifests as two microbiome state types with oral pathogens influencing severity

Mounting evidence suggests that acute appendicitis (AA) is not one but two diseases: complicated appendicitis, which is associated with necrosis leading to perforation or periappendicular abscess, and uncomplicated appendicitis, which does not necessarily result in perforation. Even though AA is the most frequent cause of surgery from abdominal pain, little is known about the origins and etiopathogenesis of this disease, much less regarding the different disease types. In this study, we investigated the microbiome of samples from the appendix, rectum and peritoneum of 60 children and adolescents with AA to assess the composition and potential function of bacteria, archaea and fungi. The analysis of the appendix microbial community revealed a shift depending on the severity of the AA. This shift was reflected by two major community state types that represented the complicated and uncomplicated cases. We could demonstrate that complicated, but not uncomplicated, appendicitis is associated with a significant local expansion of oral, bacterial pathogens in the appendix, most strongly influenced by necrotizing Fusobacterium spp., Porphyromonas and Parvimonas. Uncomplicated appendicitis, however, was characterised by gut-associated microbiomes. Our findings support the hypothesis that two disease types exist in AA, which cannot be distinguished beyond doubt using standard clinical characterization methods or by analysis of the patients rectal microbiome. An advanced microbiome diagnosis, however, could improve non-surgical treatment of uncomplicated AA. ImportanceWith a lifetime risk of up to 17%, acute appendicitis is one of the most frequent causes of emergency abdominal surgery in westernized countries. Latest literature reports suggests that appendicitis manifests in two disease types: complicated and uncomplicated appendicitis with different, yet unknown, etiopathogenesis. In this study, we investigated the microbial composition (bacteria, archaea and fungi) from 60 children and adolescents that were diagnosed with acute appendicitis. Appendix, rectal and peritoneal samples were analysed using amplicon and metagenomic sequencing. Our results suggest that acute appendicitis manifests in three microbial state types that reflect complicated and uncomplicated appendicitis as well as special cases that are caused by bacterial overgrowth. Strikingly, uncomplicated appendicitis appears to be caused by gut-associated pathogens while complicated appendicitis is driven by oral-associated microbes such as Fusobacterium sp. or Porphyromonas sp. The findings provided in our study are of special interest to understand the etiopathogenesis of both complicated and uncomplicated appendicitis.

microbiology↗

bioRxiv2020

The indoor environment - a potent source for intact human-associated anaerobes

BackgroundPeople in westernised countries spend most of their time indoors. A healthy human microbiome relies on the interaction with and exchange of microbes that takes place between the human body and its environment. For this reason, the built environment might represent a potent source of commensal microbes. Anaerobic microbes are of particular interest, as researchers have not yet sufficiently clarified how the human microbiome acquires oxygen-sensitive microbes, such as obligate or facultative anaerobes. MethodsWe sampled ten households and used propidium monoazide to assess the viability of the collected prokaryotes. We compared the microbiome profiles based on 16S rRNA gene sequencing and confirmed our results by genetic and cultivation-based analyses. ResultsQuantitative and qualitative analysis revealed that most of the microbial taxa are of human origin. Less than 25% of the prokaryotic signatures found in built environment (BE) samples originate from intact - and thus potentially living - cells, indicating that aerobic and stress resistant taxa display an apparent survival advantage. Although the dominant microbial fraction identified on the bathroom floors is composed of aerobes, we confirmed the presence of strictly anaerobic taxa, including methanogenic archaea, in PMA-treated samples. As methanogens are regarded as highly sensitive to aerobic conditions, oxygen-tolerance experiments were performed with human-associated isolates to validate their survival. These results show that these taxa have a limited but substantial ability to survive in the BE. We determined that human-associated methanogens can survive oxic conditions for at least 6 h. ConclusionsThis study enabled us to collect strong evidence that supports the hypothesis that obligate anaerobic taxa can survive in the BE for a limited amount of time. This suggests that the BE serves as a potential source of anaerobic human commensals.

microbiology↗

bioRxiv2018

Measuring the archaeome: detection and quantification of archaea signatures in the human body

Due to their fundamentally different biology, archaea are consistently overlooked in conventional 16S rRNA gene amplicon surveys. Herein, we evaluate different methodological set-ups to detect and quantify archaea signatures in human samples (nose, oral, appendix, stool, and skin) using amplicon sequencing and quantitative PCR.\n\nWith our optimized protocol, we were able to increase the detection of archaeal RSVs from one (using a so-called \"universal\" approach) to 81 RSVs in a representative sample set. Moreover, we confirmed the presence of about 5% archaeal signatures in the human gut, but found, unexpectedly, an almost 1:1 ratio of archaeal to bacterial 16S rRNA genes in appendix and nose samples. This finding indicates a high prevalence of archaeal signatures in body regions thus far not analyzed for the presence of archaea using appropriate methods.\n\nIn order to assess the archaeome diversity and archaeal abundance, a specific archaea-targeting methodology is required, for which we propose two standard procedures. These methodologies might not only prove useful for analyzing the human archaeome in more detail, but could also be used for other holobionts samples.

microbiology↗