Gastrointestinal Microbiota and Parasite-Fauna of Wild Dissostichus eleginoides Smitt, 1898 Captured at the South-Central Coast of Chile

Dissotichus eleginoides has a discontinuous circumpolar geographic distribution restricted to mountains and platforms, mainly in Subantarctic and Antarctic waters of the southern hemisphere, including the Southeast Pacific, Atlantic and Indian oceans and in areas surrounding the peninsular platforms of subantarctic islands. The aim of this work was to determine and characterize the gastrointestinal parasitic and microbial fauna of specimens of D. eleginoides captured in waters of the south-central zone of Chile. The magnitude of parasitism in D. eleginoides captured in waters of the south-central zone of Chile is variable, and the parasite richness is different from that reported in specimens from subantarctic environments. Next-generation sequencing (NGS) of the microbial community associated to intestine showed a high diversity, where Proteobacteria, Firmicutes, and Bacteriodetes were the dominant phyla. However, both parasitic and microbial structures can vary between fish from different geographic regions

Oropharynx microbiota transitions in hypopharyngeal carcinoma treatment of induced chemotherapy followed by surgery

Aims To analyze changes in oropharynx microbiota composition after receiving induced chemotherapy followed by surgery for hypopharyngeal squamous cell carcinoma (HPSCC) patients. Methods Clinical data and swab samples of 38 HPSCC patients (HPSCC group) and 30 patients with benign disease (control group, CG) were enrolled in the study. HPSCC group was stratified into two groups: induced chemotherapy group (IC) of 10 patients and non-induced chemotherapy group (nIC) of 28 patients. The microbiota from oropharyngeal membrane was analyzed through 16S rRNA sequencing. Results Alpha-diversity (Shannon and Ace indexes) and weighted UniFrac based beta-diversity severely decreased in the HPSCC group when compared with CG. In pre-operative comparisons, PCoA and NMDS analyses showed microbial structures in the IC group were more similar to CG than nIC. Both IC group and nIC group yielded significantly diverse post-operative communities in contrast to their pre-operative counterparts, evident by the decrease in genera Veillonella and Fusobacterium and increase in genera Streptococcus and Gemella. Given that post-operative oropharynx microbiota showed no difference between IC and nIC groups, the IC group showed less accumulation in anaerobic communities. The abundance of genera Fusobacterium, Parvimonas, Actinomyces were enhanced in the advanced stages (III/IV). Conclusions Oropharynx microbiota in the HPSCC group presents dysbiosis with low diversity and abundance. Induced chemotherapy is beneficial in adjusting the oropharynx microbial environment leading to fewer amounts of anaerobe accumulation after operation. Higher amounts of Fusobacterium in advanced stages (III/IV) may influence the progression of HPSCC.

Previously uncharacterized rectangular bacteria in the dolphin mouth

Much remains to be explored regarding the diversity of host-associated microbes. Here, we report the discovery of microbial structures in the mouths of bottlenose dolphins that we refer to as rectangular cell-like units (RCUs). DNA staining revealed multiple paired bands that suggested cells in the act of dividing along the longitudinal axis. Deep sequencing of samples enriched in RCUs through micromanipulation indicated that the RCUs are bacterial and distinct from Simonsiella, a genus with somewhat similar morphology and division patterning found in oral cavities of animals. Cryogenic transmission electron microscopy and tomography showed that RCUs are composed of parallel membrane-bound segments, likely individual cells, encapsulated by an S-layer-like periodic surface covering. RCUs displayed pilus-like appendages protruding as bundles of multiple threads that extend parallel to each other, and splay out at the tips and/or intertwine, in stark contrast to all known types of bacterial pili that consist of single, hair-like structures. These observations highlight the diversity of novel microbial forms and lifestyles that await discovery and characterization using tools complementary to genomics such as microscopy.

Inter-species microbiota transplantation recapitulates microbial acquisition and persistence in mosquitoes

BackgroundMosquitoes harbor microbial communities that play important roles in their growth, survival, reproduction, and ability to transmit human pathogens. Microbiome transplantation approaches are often used to study host-microbe interactions and identify microbial taxa and assemblages associated with health or disease. However, no such approaches have been developed to manipulate the microbiota of mosquitoes.ResultsHere, we developed an approach to transfer entire microbial communities between mosquito cohorts. We undertook transfers between (Culex quinquefasciatus to Aedes aegypti) and within (Ae. aegypti to Ae. aegypti) species to validate the approach and determine the number of mosquitoes required to prepare donor microbiota. After the transfer, we monitored mosquito development and microbiota dynamics throughout the life cycle. Typical holometabolous lifestyle-related microbiota structures were observed, with higher dynamics of microbial structures in larval stages, including the larval water, and less diversity in adults. Microbiota diversity in recipient adults was also more similar to the microbiota diversity in donor adults.ConclusionsThis study provides the first evidence for successful microbiome transplantation in mosquitoes. Our results highlight the value of such methods for studying mosquito-microbe interactions and lay the foundation for future studies to elucidate the factors underlying microbiota acquisition, assembly, and function in mosquitoes under controlled conditions.

The Impacts of Field Management on Soil and Tea Root Microbiomes

Due to the importance of microbes in soil health and crop production, manipulation of microbiomes provides a new strategy for improving crop growth and agricultural ecosystems. Current understanding is limited regarding the responses of soil and crop endophytic microbiomes to field management and microbiome programming. In this study, we investigated soil and tea root bacterial communities under conventional and organic cropping systems using 16S rRNA gene sequencing. A significant difference in soil and root bacterial community structure was observed under different field managements, leading to 43% and 35% variance, respectively. We also identified field management-sensitive species both in soils and tea roots that have great potential as bioindicators for bacterial microbiome manipulation. Moreover, through functional profile predictions of microbiomes, xenobiotics degradation in soil bacterial communities is enriched in organic farms, suggesting that biodegradation capabilities are enhanced under organic cropping systems. Our results demonstrate the effects of field management on both soil and tea root bacterial microbiomes and provide new insights into the reprogramming of microbial structures.

The Microbiome Profile In Ulcerative Colitis And Pouchitis

Both ulcerative colitis and pouchitis are associated with an imbalance in the intestinal microbiota, which may be related to the immune response. The objective was to determine the bacterial composition in pouchitis and ulcerative colitis in order to explore the underlying pathogenesis. Microbiome was profiled and evaluated by 16S ribosomal DNA gene sequencing in stool samples of 37 patients with ulcerative colitis, 15 patients with normal ulcerative colitis-pouch, 15 patients with ulcerative colitis-pouchitis and 18 healthy volunteers, PICRUSt and PICRUSt2 were performed to analyze the function of dominant bacteria. In our Chinese cohort, with aggravation of ulcerative colitis, intestinal microorganisms were characterized by a gradual decreased in diversity and numbers of butyrate-producing bacteria and Bacteroides. Besides, in addition to the decrease of probiotics, the bloom of Escherichia-Shigella and Ruminococcus_gnavus was observed in pouchitis which related to multiple infection pathways according to KEEG pathway analysis. Our results showed that pouchitis and ulcerative colitis differ in their intestinal microbial structures and metabolic pathways, but the reasons need to be further explored.

Preservation of Underground Microbial Diversity in Ancient Subsurface Deposits (>6 Ma) of the Rio Tinto Basement

The drilling of the Rio Tinto basement has provided evidence of an underground microbial community primarily sustained by the Fe and S metabolism through the biooxidation of pyrite orebodies. Although the gossan is the microbial activity product, which dates back to the Oligocene (25 Ma), no molecular evidence of such activity in the past has been reported yet. A Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) molecular analysis of a subsurface sample in the Peña de Hierro basement has provided novel data of the ancient underground microbial community. It shows that the microbial remains are preserved in a mineral matrix composed of laminated Fe-oxysulfates and K- and Na-bearing sulfates alternating with secondary silica. In such a mineral substrate, the biomolecule traces are found in five different microstructure associations, (1) <15 micron-sized nodular microstructures composed of POn(2≤n≤4)−, (2) <30 micron-size micronodules containing fatty acids, acylglycerides, and alkanol chains, (3) <20 micro-sized nodules containing NOn−(2≤n≤3) ions, (4) 40-micron size nodules with NH4+ and traces of peptides, and (5) >200-micron thick layer with N-bearing adducts, and sphingolipid and/or peptide traces. It suggests the mineralization of at least five microbial preserved entities with different metabolic capabilities, including: (1) Acidiphilium/Tessaracoccus-like phosphate mineralizers, (2) microbial patches preserving phosphate-free acylglycerides bacteria, (3) nitrogen oxidizing bacteria (e.g., Acidovorax sp.), (4) traces of heterotrophic ammonifying bacteria, and (5) sphingolipid bearing bacteria (e.g., Sphingomonadales, and δ-Proteobacteria) and/or mineralized biofilms. The primary biooxidation process acted as a preservation mechanism to release the inorganic ions that ultimately mineralized the microbial structures.

Deep-Sea Carbonates Are a Reservoir of Fossil Microbes Previously Inhabiting Cold Seeps

Carbonates are globally distributed particularly around deep-sea cold seeps. The embedded microbes are fossil records of the past bioprocess but metagenomes of the carbonates have not been fully studied. In this study, we report microbial community structures and genomes of dominant species in cold-seep carbonates from the South China Sea (SCS) and Gulf of Mexico (GoM). The carbonates contained both anaerobic microbes represented by methane oxidizing archaea (ANME) and aerobic ammonia-oxidizing archaea (AOA). The samples from GoM were mostly composed of small microbial groups, indicating heavy degradation of the fossil microbes. The composition of the carbonate communities differed from that of cold seep sediments, suggesting alteration of cold-seep microbial structures during formation and weathering of carbonates. Extraction of 18S rRNA genes from metagenomic reads revealed prevalence of fungal species in the carbonates of the GoM. Genome binning resulted in 10 genomes for dominant prokaryotic species. The ANME genomes showed a short genetic distance to the relatives from the current cold seep sediments; the AOA genomes were affiliated with alpha ecotype dominating deep-sea sediments. Our study reports the genomes in ancient carbonates and sheds lights on microbial role in formation and bioweathering of carbonates.