Characterization of the bacterial microbiomes of social amoebae and exploration of the roles of host and environment on microbiome composition

The ocular microbiome composition has only been partially characterized. Here, we used RNA-sequencing (RNA-Seq) data to assess microbial diversity in human corneal tissue. Additionally, conjunctival swab samples were examined to characterize ocular surface microbiota. Short RNA-Seq reads, obtained from a previous transcriptome study of 50 corneal tissues, were mapped to the human reference genome GRCh38 to remove sequences of human origin. The unmapped reads were then used for taxonomic classification by comparing them with known bacterial, archaeal, and viral sequences from public databases. The components of microbial communities were identified and characterized using both conventional microbiology and polymerase chain reaction (PCR) techniques in 36 conjunctival swabs. The majority of ocular samples examined by conventional and molecular techniques showed very similar microbial taxonomic profiles, with most of the microorganisms being classified into Proteobacteria, Firmicutes, and Actinobacteria phyla. Only 50% of conjunctival samples exhibited bacterial growth. The PCR detection provided a broader overview of positive results for conjunctival materials. The RNA-Seq assessment revealed significant variability of the corneal microbial communities, including fastidious bacteria and viruses. The use of the combined techniques allowed for a comprehensive characterization of the eye microbiome’s elements, especially in aspects of microbiota diversity.

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Characterization of the cecal microbiome composition of Wenchang chickens before and after fattening

PLoS ONE ◽

10.1371/journal.pone.0225692 ◽

2019 ◽

Vol 14 (12) ◽

pp. e0225692 ◽

Cited By ~ 1

Author(s):

Zhen Tan ◽

Lilong Luo ◽

Xiaozhe Wang ◽

Qiong Wen ◽

Lu Zhou ◽

...

Keyword(s):

Microbiome Composition ◽

Before And After

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Triparental inheritance inDictyostelium

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1814425116 ◽

2019 ◽

Vol 116 (6) ◽

pp. 2187-2192 ◽

Cited By ~ 5

Author(s):

Gareth Bloomfield ◽

Peggy Paschke ◽

Marina Okamoto ◽

Tim J. Stevens ◽

Hideko Urushihara

Keyword(s):

High Frequency ◽

Genetic Material ◽

Mitochondrial Genomes ◽

Genome Wide ◽

Organelle Genomes ◽

Initial Evolution ◽

Sexual Progeny ◽

Sexual Inheritance ◽

Social Amoebae

Sex promotes the recombination and reassortment of genetic material and is prevalent across eukaryotes, although our knowledge of the molecular details of sexual inheritance is scant in several major lineages. In social amoebae, sex involves a promiscuous mixing of cytoplasm before zygotes consume the majority of cells, but for technical reasons, sexual progeny have been difficult to obtain and study. We report here genome-wide characterization of meiotic progeny inDictyostelium discoideum. We find that recombination occurs at high frequency in pairwise crosses between all three mating types, despite the absence of the Spo11 enzyme that is normally required to initiate crossover formation. Fusions of more than two gametes to form transient syncytia lead to frequent triparental inheritance, with haploid meiotic progeny bearing recombined nuclear haplotypes from two parents and the mitochondrial genome from a third. Cells that do not contribute genetically to theDictyosteliumzygote nucleus thereby have a stake in the next haploid generation.D. discoideummitochondrial genomes are polymorphic, and our findings raise the possibility that some of this variation might be a result of sexual selection on genes that can promote the spread of individual organelle genomes during sex. This kind of self-interested mitochondrial behavior may have had important consequences during eukaryogenesis and the initial evolution of sex.

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An online atlas of human plasma metabolite signatures of gut microbiome composition

10.1101/2021.12.23.21268179 ◽

2021 ◽

Author(s):

Koen F. Dekkers ◽

Sergi Sayols-Baixeras ◽

Gabriel Baldanzi ◽

Christoph Nowak ◽

Ulf Hammar ◽

...

Keyword(s):

Gut Microbiota ◽

Gut Microbiome ◽

High Performance ◽

Alpha Diversity ◽

Plasma Metabolites ◽

Uremic Toxin ◽

Metagenomic Sequencing ◽

Microbiome Composition ◽

Plasma Metabolite

The human gut microbiota produces a variety of small compounds, some of which enter the bloodstream and impact host health. Conversely, various exogenous nutritional and pharmaceutical compounds affect the gut microbiome composition before entering circulation. Characterization of the gut microbiota—host plasma metabolite interactions is an important step towards understanding the effects of the gut microbiota on human health. However, studies involving large and deeply phenotyped cohorts that would reveal such meaningful interactions are scarce. Here, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for detailed characterization of the fecal microbiota and plasma metabolome, respectively, of 8,584 participants invited at age 50 to 64 of the Swedish CArdioPulmonary bioImage Study (SCAPIS). After adjusting for multiple comparisons, we identified 1,008 associations between species alpha diversity and plasma metabolites, and 318,944 associations between specific gut metagenomic species and plasma metabolites. The gut microbiota explained up to 50% of the variance of individual plasma metabolites (mean of 4.7%). We present all results as the searchable association atlas "GUTSY" as a rich resource for mining associations, and exemplify the potential of the atlas by presenting novel associations between oral medication and the gut microbiome, and microbiota species strongly associated with levels of the uremic toxin p-cresol sulfate. The association atlas can be used as the basis for targeted studies of perturbation of specific bacteria and for identification of candidate plasma biomarkers of gut flora composition.

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Cooperation between host immunity and the gut bacteria is essential for helminth-evoked suppression of colitis

Microbiome ◽

10.1186/s40168-021-01146-2 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Adam Shute ◽

Blanca E. Callejas ◽

ShuHua Li ◽

Arthur Wang ◽

Timothy S. Jayme ◽

...

Keyword(s):

Short Chain Fatty Acids ◽

Gut Bacteria ◽

Hymenolepis Diminuta ◽

Helminth Parasites ◽

Microbiome Composition ◽

Intention To Treat ◽

Community Profiling ◽

Epithelial Cell Lines ◽

Helminth Therapy

Abstract Background Studies on the inhibition of inflammation by infection with helminth parasites have, until recently, overlooked a key determinant of health: the gut microbiota. Infection with helminths evokes changes in the composition of their host’s microbiota: one outcome of which is an altered metabolome (e.g., levels of short-chain fatty acids (SCFAs)) in the gut lumen. The functional implications of helminth-evoked changes in the enteric microbiome (composition and metabolites) are poorly understood and are explored with respect to controlling enteric inflammation. Methods Antibiotic-treated wild-type, germ-free (GF) and free fatty-acid receptor-2 (ffar2) deficient mice were infected with the tapeworm Hymenolepis diminuta, then challenged with DNBS-colitis and disease severity and gut expression of the il-10 receptor-α and SCFA receptors/transporters assessed 3 days later. Gut bacteria composition was assessed by 16 s rRNA sequencing and SCFAs were measured. Other studies assessed the ability of feces or a bacteria-free fecal filtrate from H. diminuta-infected mice to inhibit colitis. Results Protection against disease by infection with H. diminuta was abrogated by antibiotic treatment and was not observed in GF-mice. Bacterial community profiling revealed an increase in variants belonging to the families Lachnospiraceae and Clostridium cluster XIVa in mice 8 days post-infection with H. diminuta, and the transfer of feces from these mice suppressed DNBS-colitis in GF-mice. Mice treated with a bacteria-free filtrate of feces from H. diminuta-infected mice were protected from DNBS-colitis. Metabolomic analysis revealed increased acetate and butyrate (both or which can reduce colitis) in feces from H. diminuta-infected mice, but not from antibiotic-treated H. diminuta-infected mice. H. diminuta-induced protection against DNBS-colitis was not observed in ffar2−/− mice. Immunologically, anti-il-10 antibodies inhibited the anti-colitic effect of H. diminuta-infection. Analyses of epithelial cell lines, colonoids, and colon segments uncovered reciprocity between butyrate and il-10 in the induction of the il-10-receptor and butyrate transporters. Conclusion Having defined a feed-forward signaling loop between il-10 and butyrate following infection with H. diminuta, this study identifies the gut microbiome as a critical component of the anti-colitic effect of this helminth therapy. We suggest that any intention-to-treat with helminth therapy should be based on the characterization of the patient’s immunological and microbiological response to the helminth.

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Characterization of the Gut Microbiota in Individuals with Overweight or Obesity during a Real-World Weight Loss Dietary Program: A Focus on the Bacteroides 2 Enterotype

Biomedicines ◽

10.3390/biomedicines10010016 ◽

2021 ◽

Vol 10 (1) ◽

pp. 16

Author(s):

Rohia Alili ◽

Eugeni Belda ◽

Odile Fabre ◽

Véronique Pelloux ◽

Nils Giordano ◽

...

Keyword(s):

Weight Loss ◽

Gut Microbiota ◽

Real World ◽

Dietary Intervention ◽

Streptococcus Thermophilus ◽

High Protein ◽

Microbiome Composition ◽

Low Carbohydrate ◽

Restriction Diet

Background: Dietary intervention is a cornerstone of weight loss therapies. In obesity, a dysbiotic gut microbiota (GM) is characterized by high levels of Bacteroides lineages and low diversity. We examined the GM composition changes, including the Bacteroides 2 enterotype (Bact2), in a real-world weight loss study in subjects following a high-protein hypocaloric diet with or without a live microorganisms (LMP) supplement. Method: 263 volunteers were part of this real-world weight loss program. The first phase was a high-protein low-carbohydrate calorie restriction diet with or without LMP supplements. Fecal samples were obtained at baseline and after 10% weight loss for 163 subjects. Metagenomic profiling was obtained by shotgun sequencing. Results: At baseline, the Bact2 enterotype was more prevalent in subjects with aggravated obesity and metabolic alterations. After weight loss, diversity increased and Bact2 prevalence decreased in subjects with lower GM diversity at baseline, notably in LMP consumers. Significant increases in Akkermansia muciniphila and Parabacteroides distasonis and significant decreases of Eubacterium rectale, Streptococcus thermophilus and Bifidobacterial lineages were observed after weight loss. Conclusion: Baseline microbiome composition is associated with differential changes in GM diversity and Bact2 enterotype prevalence after weight loss. Examining these signatures could drive future personalized nutrition efforts towards more favorable microbiome compositions.

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Metatranscriptomic approach for microbiome characterization and host gene expression evaluation for “Hoja de malvón” disease in Vitis vinifera cv. Malbec

10.21203/rs.3.rs-23526/v1 ◽

2020 ◽

Author(s):

Marcos Paolinelli ◽

Georgina Escoriaza ◽

Cecilia Cesari ◽

Sandra Garcia-Lampasona ◽

Rufina Hernandez-Martinez

Keyword(s):

Gene Expression ◽

Disease Process ◽

Departure Point ◽

Microbiome Composition ◽

Grapevine Trunk Diseases ◽

Advanced Stages ◽

Trunk Diseases ◽

Expression Evaluation ◽

Further Development

Abstract Background: Grapevine Trunk Diseases (GTD) threat worldwide wine and table grape production, mainly reducing grape yields and in advanced stages causing the death of diseased vines. A particular GTD of enormous concern in Argentinean vitiviniculture is the complex etiology disease locally known as "Hoja de malvón" (HDM). At least four different fungi are involved in the disease, which complicates the diagnostic and the design of strategies for vineyard management. Similar to Esca grape disease, factors that make this disease difficult to control are the presence of pathogens that not always correlates with disease symptoms or physiological changes in the host. Also the abiotic stress on grapevine seems to favors the disease process. Based on this background, it is essential to have molecular tools that allow for simultaneous explorations of the host immunity status and the microbiome composition. Results: A metatranscriptomic approach was followed and different strategies for microbiome characterization, throughmolecular marker reconstruction or unique kmer counts, were evaluated. Malbec microbiome was mainly represented for Dothideomycetes and Actinobacteria. Higher Basidiomycota/Ascomycota ratio was found in symptomatic (SYM) than in asymptomatic (ASYM) plants, with the Basidiomycota Arrambaria destruens found in higher levels in SYM plants. Besides, from mRNA-derived reads, the host functional status and main microbial functions based on gene expression were evaluated. Stress-tolerance mechanisms were activated on ASYM plants, being spermidine synthesis one of the most important, while from the microbiome side, prokaryotic tricarboxylic acid pathways were the primary differential function in SYM plants. Conclusions: This is a pioneering work for the characterization of multi-kingdom endophytic microbiome in woody tissues of grapevine cv. Malbec. Several microorganisms with negative interaction with GTD pathogens were identified and can be further explored as biological control agents for HDM disease. The integral analysis employed suggests that measuring Basidiomycota/Ascomycota ratio and spermidine-associated gene expression would help to monitor the sanitary status of grapevine and the propensity to develop HDM disease. This study provides a departure point for a better comprehension of HDM disease that can be used as a roadmap for further development of curative practices of GTD.

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Symbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential

Marine Drugs ◽

10.3390/md19070370 ◽

2021 ◽

Vol 19 (7) ◽

pp. 370

Author(s):

Ana Matos ◽

Agostinho Antunes

Keyword(s):

Marine Invertebrates ◽

Biological Functions ◽

Biotechnological Potential ◽

Symbiotic Associations ◽

Microbiome Composition ◽

Adverse Conditions ◽

Symbiotic Interactions ◽

Domains Of Life ◽

Bioactive Potential

Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has interested the scientific community, mainly due to its potential for bioactive compounds production—e.g., ET-73 (trabectedin, Yondelis), an anticancer drug. However, these symbiotic interactions embrace several environmental and biological functions with high ecological relevance, inspiring diverse biotechnological applications. We thoroughly reviewed microbiome studies (microscopic to metagenomic approaches) of around 171 hosts, worldwide dispersed, occurring at different domains of life (Archaea, Bacteria, Eukarya), to illuminate the functions and bioactive potential of associated organisms in ascidians. Associations with Bacteria are the most prevalent, namely with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria and Planctomycetes phyla. The microbiomes of ascidians belonging to Aplousobranchia order have been the most studied. The integration of worldwide studies characterizing ascidians’ microbiome composition revealed several functions including UV protection, bioaccumulation of heavy metals and defense against fouling or predators through production of natural products, chemical signals or competition. The critical assessment and characterization of these communities is extremely valuable to comprehend their biological/ecological role and biotechnological potential.

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A bacterial genome and culture collection of gut microbial in weanling piglet

10.1101/2021.08.18.456900 ◽

2021 ◽

Author(s):

Bo Dong ◽

Xiaoqian Lin ◽

Xiaohuan Jing ◽

Tongyuan Hu ◽

Jianwei Zhou ◽

...

Keyword(s):

Gut Microbiome ◽

Bacterial Genome ◽

Culture Collection ◽

Glycoside Hydrolases ◽

Individual Species ◽

Microbiome Composition ◽

Substantial Bias ◽

The Individual ◽

And Function

The microbiota hosted in the pig gastrointestinal tract are important for productivity of livestock. However, the individual species and functional repertoires that make up the pig gut microbiome remain largely undefined. Here we comprehensively investigated the genomes and functions of the piglet gut microbiome using culture-based and metagenomics approaches. A collection included 266 cultured genomes and 482 metagenome-assembled genomes (MAGs) that were clustered to 428 species across 10 phyla was established. Among these clustered species, 333 genomes represent potential new species. Less matches between cultured genomes and MAGs revealed a substantial bias for the acquisition of reference genomes by the two strategies. Glycoside hydrolases was the dominant category of carbohydrate-active enzymes. 445 secondary metabolite biosynthetic genes were predicted from 292 genomes with bacteriocin being the most. Pan genome analysis of Limosilactobacillus reuteri uncover the biosynthesis of reuterin was strain-specific and the production was experimentally determined. These genomic resources will enable a comprehensive characterization of the microbiome composition and function of pig gut.

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Transcriptomic Characterization of Tuberculous Sputum Reveals a Host Warburg Effect and Microbial Cholesterol Catabolism

mBio ◽

10.1128/mbio.01766-21 ◽

2021 ◽

Author(s):

Rachel P. J. Lai ◽

Teresa Cortes ◽

Suzaan Marais ◽

Neesha Rockwood ◽

Melissa L. Burke ◽

...

Keyword(s):

Ribosomal Dna ◽

Warburg Effect ◽

Clinical Specimens ◽

Microbiome Composition ◽

16S Ribosomal Dna ◽

Functional Inference

Although a few studies have described the microbiome composition of TB sputa based on 16S ribosomal DNA, these studies did not compare to non-TB samples and the nature of the method does not allow any functional inference. This is the first study to apply such technology using clinical specimens and obtained functional transcriptional data on all three aspects simultaneously.

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