Bela Hausmann

Phylogeny- or activity-based fluorescent labelling of microorganisms coupled with fluorescence activated cell sorting (FACS) is a powerful approach to rapidly isolate cells of interest from complex communities for targeted genomics. However, the method has not been widely adopted because standard paraformaldehyde or ethanol fixation procedures hamper nucleic acid recovery and/or long-term sample storage. Here, we present dithiobis(succinimidyl propionate) (DSP) as a reversible fixative for microbial cells that enables fluorescence imaging and DNA extraction and amplification for sequencing. DSP fixation is compatible with widely used fluorescence in situ hybridization (FISH) approaches and bioorthogonal non-canonical amino acid tagging, and can be applied to diverse sample types, where it consistently performed as well as paraformaldehyde. Furthermore, high-quality genomes were obtained from individual and multiple bacterial cells selectively extracted from complex samples using FISH-FACS. Thus, DSP is a dual-use fixative for microbiome imaging and sequencing, improving targeted microbial genomics.

Fecal microbiota transplantation (FMT) may help to overcome resistance to immunotherapy. In this single-center, single-arm phase II hypothesis-generating pilot study (FAB-HCC), we included 12 patients with advanced hepatocellular carcinoma (HCC) who progressed on atezolizumab plus bevacizumab. Patients received a single FMT via colonoscopy from a donor with HCC who responded to anti-PD-1 treatment or a healthy donor, combined with atezolizumab plus bevacizumab. The primary endpoint was safety as measured by incidence and severity of treatment-related adverse events (TRAEs). Secondary endpoints included radiological response and survival. Grade 3-4 TRAEs included arterial hypertension ( n = 5) and proteinuria ( n = 3), both related to bevacizumab, and diarrhea ( n = 1), related to FMT. No serious TRAEs were observed. Objective response rate was 33% ( n = 4/12) and median progression-free survival was 6.9 (95%CI, 3.0-10.8) months. Following FMT, recipient microbiome composition appeared more similar to that of the donor, and healthy donor FMT seemed to be associated with higher engraftment. FMT appeared to be associated with enrichment of response-associated and loss of deleterious gut bacteria. Circulating PD-1 ⁺ CD8 ⁺ T cells decreased and CD32b ⁺ CD14 ^high CD16 ^low monocytes increased following FMT plus immunotherapy. Phage-display immunoprecipitation sequencing revealed that antibody repertoire stability, rather than global diversity or composition, changed over time. Taken together, FMT combined with atezolizumab plus bevacizumab was safe and associated with a high response rate in patients with atezolizumab plus bevacizumab-refractory HCC. Given the limited sample size, these findings need cautious interpretation and confirmation in larger, adequately powered trials. ClinicalTrials.gov identifier: NCT05750030.

Nematodes play key roles in natural and agricultural ecosystems. They contribute to organic matter transformation and the stability of soil food webs. Beyond their free-living forms, many nematode lineages have evolved in close associations with insects, ranging from mutualistic and commensal to parasitic interactions. Recent studies have revealed that nematodes are common in tropical ant–plant mutualisms and are particularly relevant in ant-made organic matter piles, or “patches”, within ant nests. To investigate nematode community dynamics during ant colony growth and their consistency across closely related ant species, we analysed patches from 65 ant colonies of the Azteca-Cecropia ant-plant mutualism using 18S rRNA metabarcoding combined with morphology-based quantification methods. Bacterivorous nematodes from the order Rhabditida were present in all samples, regardless of the ant or plant species and the colony developmental stage. Members of Tylenchida and Dorylaimida were also detected, though sporadically. Our results support the previously proposed vertical transmission of bacterivorous nematodes from mother to daughter colonies as well as horizontal transmission among patches within the same ant colony. Moreover, nematode community composition remained stable throughout colony development but varied between ant species. These findings demonstrate that nematodes constitute a persistent and functionally important component of this ant–plant mutualism.

Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a “three-way” facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Candidatus Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots, raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S ribosomal RNA (rRNA) gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.

Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.

Soil organic matter is the largest terrestrial reservoir of organic carbon. Its particulate fraction, particulate organic matter (POM), serves as a resource and surface for microbial colonization. Degradation of complex biopolymers like cellulose and chitin requires extracellular enzymes produced by phylogenetically diverse microbes. Despite their importance for carbon cycling, the structure and spatio-temporal dynamics of POM-associated microbial communities in soil and how specific substrates influence them remain poorly understood. This study investigated whether microbial communities associated with POM change in composition and richness over time and whether chitin and cellulose select for distinct fungal and bacterial taxa. We incubated self-manufactured, millimeter-sized model substrate particles containing chitin or cellulose in soil under laboratory and field conditions. We assessed particle-associated communities at multiple time points over a 50-day-long incubation in the lab and after 47 days in the field. Our results show that community structure and temporal dynamics of particle-associated microbial communities were substrate-specific. While microbial biomass increased on both particle types, chitin-associated microbial communities exhibited stronger temporal changes. Communities on chitin and cellulose particles were enriched in specific bacterial and fungal genera compared to communities in the surrounding soil. We demonstrate that microbial communities associated with model chitin particles underwent notable temporal changes, including decreased microbial richness and shifts in community composition over the incubation period. This study shows the potential of model particles to advance our understanding of particle- and substrate-associated microbial communities in soil.

Recent studies have suggested associations between consistent inter-individual behavioral variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated associations between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status, and relatedness of 26 captive common marmosets ( Callithrix jacchus ), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genus Desulfovibrio were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene dsrB confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between identified microbial taxa and personality traits in captive common marmosets. IMPORTANCE: This study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential of the gut microbiome to reflect or be associated with personality differences. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.

Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a ‘three-way’ facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Ca . Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S rRNA amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea. We show that two of the Ca . Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two species, which has important evolutionary and ecological implications for both hosts and symbionts, as well as thin response to climate change.

Soil organic matter is the largest terrestrial reservoir of organic carbon. Its particulate fraction, particulate organic matter (POM), serves as a resource and surface for microbial colonization. Degradation of complex biopolymers like cellulose and chitin requires extracellular enzymes produced by phylogenetically diverse microbes. Despite their importance for carbon cycling, the structure and spatio-temporal dynamics of POM-associated microbial communities in soil and how specific substrates influence them remain poorly understood. This study investigated whether microbial communities associated with POM change in composition and richness over time and whether chitin and cellulose select for distinct fungal and bacterial taxa. We incubated self-manufactured, millimetre-sized model substrate particles containing chitin or cellulose in soil under laboratory and field conditions. We assessed particle-associated communities at multiple time points over a 50-day-long incubation in the lab and after 47 days in the field. Our results show that community structure and temporal dynamics of particle-associated microbial communities were substrate-specific. While microbial biomass increased on both particle types, chitin-associated microbial communities exhibited stronger temporal changes. Communities on chitin and cellulose particles were enriched in specific bacterial and fungal genera compared to communities in the surrounding soil. We demonstrate that microbial communities associated with model chitin particles underwent notable temporal changes, including decreased microbial richness and shifts in community composition over the incubation period. This study shows the potential of model particles to advance our understanding of particle- and substrate-associated microbial communities in soil.

Patho-mechanistic origins of ulcerative colitis are still poorly understood. The actin cross-linker filamin A (FLNA) impacts cellular responses through interaction with cytosolic proteins. Posttranscriptional A-to-I editing generates two forms of FLNA: genome-encoded FLNAQ and FLNAR. FLNA is edited in colon fibroblasts, smooth muscle cells, and endothelial cells. We found that the FLNA editing status determines colitis severity. Editing was highest in healthy colons and reduced during murine and human colitis. Mice that exclusively express FLNAR were highly resistant to DSS-induced colitis, whereas fully FLNAQ animals developed severe inflammation. While the genetic induction of FLNA editing influenced transcriptional states of structural cells and microbiome composition, we found that FLNAR exerts protection specifically via myeloid cells, which are physiologically unedited. Introducing fixed FLNAR did not hamper cell migration but reduced macrophage inflammation and rendered neutrophils less prone to NETosis. Thus, loss of FLNA editing correlates with colitis severity, and targeted editing of myeloid cells serves as a novel therapeutic approach in intestinal inflammation.