Constructing a Defined Starter for Multispecies Vinegar Fermentation via Evaluating the Vitality and Dominance of Functional Microbes in Autochthonous Starter

Mature vinegar culture has usually been used as a type of autochthonous starter for rapidly initiate initiating the next batch of acetic acid fermentation (AAF) and maintaining the batch-to-batch uniformity of AAF in the production of traditional cereal vinegar. However, the vitality and dominance of functional microbes in autochthonous starters remain unclear, which hinders further improvement of fermentation yield and production. Here, based on metagenomic (MG), metatranscriptomic (MT), and 16S rRNA gene sequencings, 11 bacterial operational taxonomic units (OTUs) with significant metabolic activity (MT/MG ratio >1) and dominance (relative abundance >1%) were targeted in the autochthonous vinegar starter, all of which were assigned to 4 species ( Acetobacter pasteurianus , Lactobacillus acetotolerans , L. helveticus , Acetilactobacillus jinshanensis ). Then, we evaluated the successions and interactions of these 11 bacterial OTUs at different AAF stages. Last, a defined starter was constructed with 4 core species isolated from the autochthonous starter ( A. pasteurianus , L. acetotolerans , L. helveticus , Ac. jinshanensis ). The defined starter culture could rapidly initiate the AAF in a sterile or unsterilized environment and similar dynamics of metabolites (ethanol, titratable acidity, acetic acid, lactic acid, and volatile compounds) and environmental indexes (temperature, pH) of fermentation were observed as compared with that of autochthonous starter ( P > 0.05). This work provides a method to construct a defined microbiota from a complex system while preserving its metabolic function. IMPORTANCE Complex microorganisms are beneficial to the flavor formation in natural food fermentation, but they also pose challenges to the mass production of standardized products. It is attractive to construct a defined starter to rapidly initiate fermentation process and significantly improve fermentation yield. This study provides a comprehensive understanding of vital and dominant species in the autochthonous vinegar starter via multi-omics, and designs a defined microbial community for the efficient fermentation of cereal vinegar.

Helminths and helminth communities of Carassius gibelio (Bloch, 1782) from the Panicheri Reservoir, Aegean Water Basin, Bulgaria

Ecologoparasitological research was done based on the helminths and helminth communities of the Prussian carp (Carassius gibelio (Bloch, 1782)) from the freshwater ecosystem of the Panicheri Reservoir, Aegean Water Basin, Bulgaria. As a result of the examined nine specimens of the Prussian carp, two species of helminths were found: Ligula intestinalis (Linnaeus, 1758), larvae and Pomphorhynchus laevis (Müller, 1776). The dominant structure of the helminth communities was determined. The Panicheri Reservoir is a new habitat in Bulgaria of P. laevis and L. intestinalis from C. gibelio. C. gibelio is a new host record for L. intestinalis in Bulgaria. The two helminth species are core species for the helminth communities of the examined species of the freshwater fish. P. laevis was distinguished with higher prevalence and mean intensity (P%=33.34; MI=1.34) than L. intestinalis (P%=22.23; MI=1.0). The circulatory pathways of the helminth flow were traced.

Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes

Microbial communities normally comprise a few core species and large numbers of satellite species. These two sub-communities have different ecological and functional roles in natural environments, but knowledge on the assembly processes and co-occurrence patterns of the core and satellite species in Tibetan lakes is still sparse. Here, we investigated the ecological processes and co-occurrence relationships of the core and satellite bacterial sub-communities in the Tibetan lakes via 454 sequencing of 16S rRNA gene. Our studies indicated that the core and satellite bacterial sub-communities have similar dominant phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). But the core sub-communities were less diverse and exhibited a stronger distance-decay relationship than the satellite sub-communities. In addition, topological properties of nodes in the network demonstrated that the core sub-communities had more complex and stable co-occurrence associations and were primarily driven by stochastic processes (58.19%). By contrast, the satellite sub-communities were mainly governed by deterministic processes (62.17%). Overall, this study demonstrated the differences in the core and satellite sub-community assembly and network stability, suggesting the importance of considering species traits to understand the biogeographic distribution of bacterial communities in high-altitude lakes.

An Ifnar1 allele impairs the colonization of gut bacteria and promotes tuberculosis

Both host genetics and gut microbiome have important effects on human health, yet how host genetics regulates gut bacteria and further determines disease susceptibility remains unclear. Here, we find that gut microbiome pattern of active tuberculosis (TB) patients is characterized by a reduction of core species found across healthy controls, particularly Akkermansia muciniphila (A. muciniphila). Oral treatments of A. muciniphila or palmitoleic acid, an A. muciniphila-derived metabolite, strongly inhibit TB infection through epigenetically inhibiting TNF-α. We use three independent cohorts comprising 6512 individuals and identify that single-nucleotide polymorphism rs2257167 “G” allele of type I interferon (IFN-I) receptor 1 (Ifnar1) contributes to stronger IFN-I signaling, impaired colonization and abundance of A. muciniphila, reduced production of palmitoleic acid, higher TNF-α, and much severer TB disease in humans and transgenic mice. Thus, host genetics are critical in modulating structure and functions of gut microbiome and gut microbial metabolites, which further determines disease susceptibility.

Completeness of rapid assessments of medium and large mammal diversity in the northwestern Amazon in Colombia

ABSTRACT Rapid assessments are the most common information source on biodiversity in the northwestern Amazon in Colombia due to limited resources and logistic constraints. These assessments are essential for decision-making on environmental policies in this region, that has been strongly impacted by the transformation of its natural ecosystems. Several local camera-trapping rapid assessments of medium and large-sized mammals (MLM) have been conducted in the Colombian Amazon, but they are difficult to compare. We analyzed information of 16 of these rapid assessments of MLM to provide the first list of MLM in the northwestern Amazon in Colombia. We also evaluated the accuracy of four estimators (ICE, Chao-2, Jackknife-1, and Jackknife-2), and the minimum sampling effort for the estimation of MLM richness in local surveys in the region. We report 26 species of MLM for the Colombian Amazon (between five and 13 species per locality), which is an underestimation of MLM richness in the region. The best estimator of MLM richness was the Jackknife-1, due to its precision and the lower influence of singletons. We recommend a minimum sampling effort of 350 camera trap-days. Although rapid assessments do not allow a robust estimation of MLM richness, they record the most common species (or core species) per locality and their abundance variation. The evaluation of the effect of habitat transformation on MLM and the estimation of population parameters of rare species require more intensive studies.

Disruption of Traditional Grazing and Fire Regimes Shape the Fungal Endophyte Assemblages of the Tall-Grass Brachypodium rupestre

The plant microbiome is likely to play a key role in the resilience of communities to the global climate change. This research analyses the culturable fungal mycobiota of Brachypodium rupestre across a sharp gradient of disturbance caused by an intense, anthropogenic fire regime. This factor has dramatic consequences for the community composition and diversity of high-altitude grasslands in the Pyrenees. Plants were sampled at six sites, and the fungal assemblages of shoots, rhizomes, and roots were characterized by culture-dependent techniques. Compared to other co-occurring grasses, B. rupestre hosted a poorer mycobiome which consisted of many rare species and a few core species that differed between aerial and belowground tissues. Recurrent burnings did not affect the diversity of the endophyte assemblages, but the percentages of infection of two core species -Omnidemptus graminis and Lachnum sp. -increased significantly. The patterns observed might be explained by (1) the capacity to survive in belowground tissues during winter and rapidly spread to the shoots when the grass starts its spring growth (O. graminis), and (2) the location in belowground tissues and its resistance to stress (Lachnum sp.). Future work should address whether the enhanced taxa have a role in the expansive success of B. rupestre in these anthropized environments.

Heterogeneity and Chemical Reactivity of the Remote Troposphere defined by Aircraft Measurements

The NASA Atmospheric Tomography (ATom) mission built a photochemical climatology of air parcels based on in situ measurements with the NASA DC-8 aircraft along objectively planned profiling transects through the middle of the Pacific and Atlantic Oceans. ATom measured numerous gases and aerosols, particularly the gaseous species driving the chemical budgets of O3 and CH4: i.e., O3, CH4, CO, C2H6, higher alkanes, alkenes, aromatics, NOx, HNO3, HNO4, peroxyacetylnitrate, other organic nitrates, H2O, HCHO, H2O2, and CH3OOH. From the 10 s (2 km) merged observations, a modeling data stream (MDS) based on observations of the core species, consisting of 146,494 distinct air parcels has been constructed from the 4 ATom deployments, providing a continuous data stream for initializing global chemistry models and calculating the 24-hour chemical tendencies. Tendencies derived from 6 chemistry models using the ATom-1 MDS tend to agree and show a highly heterogeneous troposphere where globally 10% of the parcels control as much as 40% of the budget of O3 and CH4. Surprisingly, modeled probability distributions (100-km cells) match ATom statistics (2 km parcels), indicating that the majority of the observed heterogeneity can be resolved with current global chemistry models. On the other hand, the models' own chemical climatologies underestimate O3 production below 4 km in both Pacific and Atlantic basins because they have lower NOX levels than observed.

Identification of Microbiome Etiology Associated With Drug Resistance in Pleural Empyema

Identification of the offending organism and appropriate antimicrobial therapy are crucial for treating empyema. Diagnosis of empyema is largely obscured by the conventional bacterial cultivation and PCR process that has relatively low sensitivity, leading to limited understanding of the etiopathogenesis, microbiology, and role of antibiotics in the pleural cavity. To expand our understanding of its pathophysiology, we have carried out a metagenomic snapshot of the pleural effusion from 45 empyema patients by Illumina sequencing platform to assess its taxonomic, and antibiotic resistome structure. Our results showed that the variation of microbiota in the pleural effusion is generally stratified, not continuous. There are two distinct microbiome clusters observed in the forty-five samples: HA-SA type and LA-SA type. The categorization is mostly driven by species composition: HA-SA type is marked by Staphylococcus aureus as the core species, with other enriched 6 bacteria and 3 fungi, forming a low diversity and highly stable microbial community; whereas the LA-SA type has a more diverse microbial community with a distinct set of bacterial species that are assumed to be the oral origin. The microbial community does not shape the dominant antibiotic resistance classes which were common in the two types, while the increase of microbial diversity was correlated with the increase in antibiotic resistance genes. The existence of well-balanced microbial symbiotic states might respond differently to pathogen colonization and drug intake. This study provides a deeper understanding of the pathobiology of pleural empyema and suggests that potential resistance genes may hinder the antimicrobial therapy of empyema.

Application of Next-Generation Sequencing for the Determination of the Bacterial Community in the Gut Contents of Brackish Copepod Species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus)

The gut bacterial communities of copepods can affect metabolic processes, and consequently, their activity can be related to the release of organic substances to the environment. Hence, they are important for organic matter cycling in marine coast food webs. However, information regarding the variation in gut bacterial communities based on copepod species and environmental variations is limited. We analysed the differences in gut bacterial communities from dominant copepod species, i.e., Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus, in a brackish reservoir. The core bacteria among the copepod species and locations consisted of the following main operational taxonomic units (OTUs): Novosphingobium capsulatum and the family Rhodobacteraceae belonging to Alphaproteobacteria, which is abundant in seawater and freshwater aquatic ecosystems as a zooplankton-associated bacterial community. The bacterial community composition of each copepod (except the core species) showed high variability. The bacterial community diversity differed depending on the copepod species and the sites’ environmental conditions, especially salinity, e.g., compositional variations in the bacterial community of P. inopinus were high at sites with low salinity. Therefore, the gut bacterial community of each copepod species responds differently to the environment.