Deciphering the interdependent labyrinth between gut microbiota and the immune system.

The human gut microbiome interacts with each other and the host, which has significant effects on health and disease development. Intestinal homeostasis and inflammation are maintained by the dynamic interactions between gut microbiota and the innate and adaptive immune systems. Numerous metabolic products produced by the gut microbiota play a role in mediating cross-talk between gut epithelial and immune cells. In the event of an imbalance between the immune system and microbiota, the body becomes susceptible to infections and homeostasis is compromised. This review mainly focuses on the interplay between microbes and the immune system, such as T-cell- and B-cell-mediated adaptive responses to microbiota and signalling pathways for effective communication between the two. We have also highlighted the role of microbes in the activation of the immune response, the development of memory cells and how the immune system determines the diversity of human gut microbiota. The review also explains the relationship of commensal microbiota and their relation to the production of immunoglobulins.

Tephritid-microbial interactions to enhance fruit fly performance in sterile insect technique programs.

BACKGROUND: The Sterile Insect Technique (SIT) is being applied for the management of economically important pest fruit flies (Diptera: Tephritidae) in a number of countries worldwide. The success and cost effectiveness of SIT depends upon the ability of mass-reared sterilized male insects to successfully copulate with conspecific wild fertile females when released in the field. METHODS: We conducted a critical analysis of the literature about the tephritid gut microbiome including the advancement of methods for the identification and characterization of microbiota, particularly next generation sequencing, the impacts of irradiation (to induce sterility of flies) and fruit fly rearing, and the use of probiotics to manipulate the fruit fly gut microbiota. RESULTS: Domestication, mass-rearing, irradiation and handling, as required in SIT, may change the structure of the fruit flies' gut microbial community compared to that of wild flies under field conditions. Gut microbiota of tephritids are important in their hosts' development, performance and physiology. Knowledge of how mass-rearing and associated changes of the microbial community impact the functional role of the bacteria and host biology is limited. Probiotics offer potential to encourage a gut microbial community that limits pathogens, and improves the quality of fruit flies. CONCLUSIONS: Advances in technologies used to identify and characterize the gut microbiota will continue to expand our understanding of tephritid gut microbial diversity and community composition. Knowledge about the functions of gut microbes will increase through the use of gnotobiotic models, genome sequencing, metagenomics, metatranscriptomics, metabolomics and metaproteomics. The use of probiotics, or manipulation of the gut microbiota, offers significant opportunities to enhance the production of high quality, performing fruit flies in operational SIT programs.

Trichomonas vaginalis and Mycoplasma hominis: new tales of two old friends.

Trichomonas vaginalis is an anaerobic protist, responsible for the most prevalent non-viral sexually transmitted infection in humans. One of the most intriguing aspects of T. vaginalis pathobiology is the complex relationship with intracellular microbial symbionts: a group of dsRNA viruses belonging to family of Totiviridae (T. vaginalis virus), and eubacteria belonging to the Mycoplasma genus, in particular Mycoplasma hominis. Both microorganisms seem to strongly influence the lifestyle of T. vaginalis, suggesting a role of the symbiosis in the high variability of clinical presentation and sequelae during trichomoniasis. In the last few years many aspects of this unique symbiotic relationship have been investigated: M. hominis resides and replicates in the protozoan cell, and T. vaginalis is able to pass the bacterial infection to both mycoplasma-free protozoan isolates and human epithelial cells; M. hominis synergistically upregulates the proinflammatory response of human monocytes to T. vaginalis. Furthermore, the influence of M. hominis over T. vaginalis metabolism and physiology has been characterized. The identification of a novel species belonging to the class of Mollicutes (Candidatus Mycoplasma girerdii) exclusively associated to T. vaginalis opens new perspectives in the research of the complex series of events taking place in the multifaceted world of the vaginal microbiota, both under normal and pathological conditions.

A novel experimental system using the liverwort Marchantia polymorpha and its fungal endophytes reveals diverse and context-dependent effects.

Fungal symbioses are ubiquitous in plants, but their effects have mostly been studied in seed plants. This study aimed to assess the diversity of fungal endophyte effects in a bryophyte and identify factors contributing to the variability of outcomes in these interactions. Fungal endophyte cultures and axenic liverwort clones were isolated from wild populations of the liverwort, Marchantia polymorpha. These collections were combined in a gnotobiotic system to test the effects of fungal isolates on the growth rates of hosts under laboratory conditions. Under the experimental conditions, fungi isolated from M. polymorpha ranged from aggressively pathogenic to strongly growth-promoting, but the majority of isolates caused no detectable change in host growth. Growth promotion by selected fungi depended on nutrient concentrations and was inhibited by coinoculation with multiple fungi. The M. polymorpha endophyte system expands the resources for this model liverwort. The experiments presented here demonstrate a wealth of diversity in fungal interactions even in a host reported to lack standard mycorrhizal symbiosis. In addition, they show that some known pathogens of vascular plants live in M. polymorpha and can confer benefits to this nonvascular host. This highlights the importance of studying endophyte effects across the plant tree of life.

Widespread occurrence of the antifungal cutaneous bacterium Janthinobacterium lividum on Andean water frogs threatened by fungal disease.

Amphibian diversity has declined due to the infectious disease chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). Coexistence between amphibian hosts and this pathogen in some locations is attributed to the presence of the cutaneous bacterium Janthinobacterium lividum (Jliv). This microbe inhibits the growth of Bd on the host, reduces morbidity, and improves survival. Andean water frogs in the genus Telmatobius seem to be particularly vulnerable to the disease yet populations of T. intermedius and T. marmoratus persist in southern and central Peru. We investigated the presence of Jliv on these 2 frog species and assessed the relationship of Jliv presence with prevalence and intensity of Bd infection. By sampling 125 frogs from 7 streams (3323-3950 m a.s.l.) and 27 from a city market, we found spatial variation in the mutualism among populations (range 0-40% proportion of Jliv-positives). Overall, 57% of frogs were infected with Bd, 12.5% of frogs hosted both Jliv and Bd, while 7.2% hosted just Jliv. We found that the probability of an individual being infected with Bd was independent of the presence of Jliv; however, we did detect a protective effect of Jliv with respect to intensity of infection. The extent of Jliv distribution in the high Andes stands in stark contrast to the rarity of Jliv on frogs in lower elevation cloud forest biomes.

Microbiological, biochemical, and functional aspects of sugary kefir fermentation - A review.

Sugary kefir beverage is produce by fermenting raw sugar solution with kefir grains, the latter consisting of polysaccharide and microorganisms. This beverage, with great consumption in countries such as USA, Japan, France, and Brazil, represents a promising market to functional cultured drinks. This paper reviews the microbial diversity and interaction, kinetics, safety, and bioactivities of sugary kefir fermentation. The literature reviewed here demonstrates that sugary kefir possesses a similar microbial association relative to traditional milk kefir fermentation, especially among lactic acid bacteria and yeast species, such as Lactobacillus, Leuconostoc, Kluyveromyces, Pichia, and Saccharomyces. However, a selective pressure at species level is generally observed, as, for example, the stimulation of Saccharomyces species metabolism, leading to a high content of alcohol in the final product. This also seems to stimulate the growth of acetic acid bacteria that benefit of increased ethanol production to acetic acid metabolism. Existing reports have suggested important bioactivities associated with sugary kefir beverage consumption, such as antimicrobial, antiedematogenic, anti-inflammatory, antioxidant, cicatrizing, and healing activities. Other alternative non-dairy substrates, such as fruits, vegetables, and molasses, have also been tested for adaptation of kefir grains and production of functional beverages with distinct sensory characteristics. This diversification is of crucial importance for the production of new probiotic products to provide people with special needs (lactose intolerance) and vegan consumers.

Physiology of environmental adaptations and resource acquisition in cockroaches.

Cockroaches are a group of insects that evolved early in geological time. Because of their antiquity, they for the most part display generalized behavior and physiology and accordingly have frequently been used as model insects to examine physiological and biochemical mechanisms involved with water balance, nutrition, reproduction, genetics, and insecticide resistance. As a result, a considerable amount of information on these topics is available. However, there is much more to be learned by employing new protocols, microchemical analytical techniques, and molecular biology tools to explore many unanswered questions.

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture.

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.

A systematic discussion and comparison of the construction methods of synthetic microbial community.

Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.

Frenemies on the reef? Resolving the coral-Endozoicomonas association.

Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.

Advanced nitrogen and phosphorus removal by the symbiosis of PAOs, DPAOs and DGAOs in a pilot-scale A2O/A+MBR process with a low C/N ratio of influent.

Cooperating in harmony to avoid competition with dominant functional microbial symbiosis is an efficient way in advanced nitrogen and phosphorus removal in wastewater treatment processes. In this study, a niche-based coordinating strategy was implemented to cooperate in harmony with phosphorus-accumulating organisms (PAOs), denitrifying phosphorus-accumulating organisms (DPAOs) and denitrifying glycogen-accumulating organisms (DGAOs) to advance nitrogen and phosphorus removal based on an anaerobic-anoxic-oxic-anoxic-membrane bioreactor (A2O/A+MBR) under low C/N in municipal wastewater influent. The niche-based strategy was conducted based on the ORP change during the process as an indicator combined with the adjustment of recirculation and anoxic zone shifting. The results indicated that the strategy of the post-anoxic unit could enable significant enhancement of biological nitrogen and phosphorus removal (BNPR) by 9.9% and 16.3%, respectively, with low effluent concentrations of 7.0 ± 2.2 mg N/L and 0.36±0.32 mg P/L. The satisfactory performance was dominated along with the shift in the microbial community: the relative abundance of Tetrasphaera (PAO genus) increased from 0.14±0.08% to 0.32±0.12%, while the relative abundance of Decchloromonas (DGAO genus) and Candidatus Competibacter (DGAO genus) also increased. The advanced combination of anaerobic phosphorus release, anoxic denitrification, denitrifying phosphorus removal and endogenous denitrification was qualified by the modeling simulation of the biochemical kinetics mechanism of activated sludge in the A2O+MBR and A2O/A+MBR processes, which means that cooperation in the harmony of PAOs, DPAOs and DGAOs could be efficiently realized by a promising control strategy to enhance BNPR in an A2O+MBR with a post-anoxic unit. This study provides an efficient and simple novel control strategy to overcome the limitation of traditional nitrogen and phosphorus removal under an insufficient carbon source.

Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health.

A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.

Acanthamoeba, an environmental phagocyte enhancing survival and transmission of human pathogens.

The opportunistic protist Acanthamoeba, which interacts with other microbes such as bacteria, fungi, and viruses, shows significant similarity in cellular and functional aspects to human macrophages. Intracellular survival of microbes in this microbivorous amoebal host may be a crucial step for initiation of infection in higher eukaryotic cells. Therefore, Acanthamoeba-microbe adaptations are considered an evolutionary model of macrophage-pathogen interactions. This paper reviews Acanthamoeba as an emerging human pathogen and different ecological interactions between Acanthamoeba and microbes that may serve as environmental training grounds and a genetic melting pot for the evolution, persistence, and transmission of potential human pathogens.

FtsZ-mediated fission of a cuboid bacterial symbiont.

Less than a handful of cuboid and squared cells have been described in nature, which makes them a rarity. Here, we show how Candidatus Thiosymbion cuboideus, a cube-like gammaproteobacterium, reproduces on the surface of marine free-living nematodes. Immunostaining of symbiont cells with an anti-fimbriae antibody revealed that they are host-polarized, as these appendages exclusively localized at the host-proximal (animal-attached) pole. Moreover, by applying a fluorescently labeled metabolic probe to track new cell wall insertion in vivo, we observed that the host-attached pole started septation before the distal one. Similarly, Ca. T. cuboideus cells immunostained with an anti-FtsZ antibody revealed a proximal-to-distal localization pattern of this tubulin homolog. Although FtsZ has been shown to arrange into squares in synthetically remodeled cuboid cells, here we show that FtsZ may also mediate the division of naturally occurring ones. This implies that, even in natural settings, membrane roundness is not required for FtsZ function.

Algal p-coumaric acid induces oxidative stress and siderophore biosynthesis in the bacterial symbiont Phaeobacter inhibens.

The marine alpha-proteobacterium Phaeobacter inhibens engages in intermittent symbioses with microalgae. The symbiosis is biphasic and concludes in a parasitic phase, during which the bacteria release algaecidal metabolites in response to algal p-coumaric acid (pCA). The cell-wide effects of pCA on P. inhibens remain unknown. Herein, we report a microarray-based transcriptomic study and find that genes related to the oxidative stress response and secondary metabolism are upregulated most, while those associated with energy production and motility are downregulated in the presence of pCA. Among genes upregulated is a previously unannotated biosynthetic gene cluster and, using a combination of gene deletions and metabolic profiling, we show that it gives rise to an unreported siderophore, roseobactin. The simultaneous production of algaecides and roseobactin in the parasitic phase allows the bacteria to take up any iron that is released from dying algal cells, thereby securing a limited micronutrient.

Host Microbiota Balance in Teenagers with Gum Hypertrophy Concomitant with Acne Vulgaris: Role of Oral Hygiene Associated with Topical Probiotics.

Gum hypertrophy is a very frequent condition linked to orthodontic treatment, especially in teenagers, and the same time, about 80% of young adults are affected by acne vulgaris, a chronic inflammatory skin disease, typically treated with antibacterial therapy. The use of probiotics has gained popularity in the medical field, and many studies have demonstrated its effectiveness, such as the positive effects of some bacterial strains belonging to Lactobacillus species. The aim of this study is to document the effect of Lactobacillus reuteri (L. reuteri) on facial skin that was randomly observed in two orthodontic patients. We present two case reports of a 14-year-old female patient and a 15-year-old male patient suffering from acne vulgaris who, during fixed orthodontic treatment, showed clinical signs of gingivitis with high values of Full Mouth Plaque Score (FMPS) and Bleeding on Probing (BOP). The patients were treated first with professional oral hygiene sessions and Scaling and Root Planing (SRP) procedures, and then with the administration of a formulate containing L. reuteri as a probiotic. The follow-up was made at four weeks. During the follow-up analysis, both patients showed a significant clinical remission for gum hypertrophy and skin acne vulgaris.

Dysregulation of host-control causes interspecific conflict over host investment into symbiotic organs.

Microbial mutualists provide substantial benefits to hosts that feed back to enhance the fitness of the associated microbes. In many systems, beneficial microbes colonize symbiotic organs, specialized host structures that house symbionts and mediate resources exchanged between parties. Mutualisms are characterized by net benefits exchanged among members of different species, however, inequalities in the magnitude of these exchanges could result in evolutionary conflict, destabilizing the mutualism. We investigated joint fitness effects of root nodule formation, the symbiotic organ of legumes that house nitrogen-fixing rhizobia in planta. We quantified host and symbiont fitness parameters dependent on the number of nodules formed using near-isogenic Lotus japonicus and Mesorhizobium loti mutants, respectively. Empirically estimated fitness functions suggest that legume and rhizobia fitness is aligned as the number of nodules formed increases from zero until the host optimum is reached, a point where aligned fitness interests shift to diverging fitness interests between host and symbiont. However, fitness conflict was only inferred when analyzing wild-type hosts along with their mutants dysregulated for control over nodule formation. These data demonstrate that to avoid conflict, hosts must tightly regulate investment into symbiotic organs maximizing their benefit to cost ratio of associating with microbes.

Experimental Warming Reduces Survival, Cold Tolerance, and Gut Prokaryotic Diversity of the Eastern Subterranean Termite, Reticulitermes flavipes (Kollar).

Understanding the effects of environmental disturbances on insects is crucial in predicting the impact of climate change on their distribution, abundance, and ecology. As microbial symbionts are known to play an integral role in a diversity of functions within the insect host, research examining how organisms adapt to environmental fluctuations should include their associated microbiota. In this study, subterranean termites [Reticulitermes flavipes (Kollar)] were exposed to three different temperature treatments characterized as low (15°C), medium (27°C), and high (35°C). Results suggested that pre-exposure to cold allowed termites to stay active longer in decreasing temperatures but caused termites to freeze at higher temperatures. High temperature exposure had the most deleterious effects on termites with a significant reduction in termite survival as well as reduced ability to withstand cold stress. The microbial community of high temperature exposed termites also showed a reduction in bacterial richness and decreased relative abundance of Spirochaetes, Elusimicrobia, and methanogenic Euryarchaeota. Our results indicate a potential link between gut bacterial symbionts and termite's physiological response to environmental changes and highlight the need to consider microbial symbionts in studies relating to insect thermosensitivity.

Syntrophic metabolism facilitates Methanosarcina-led methanation in the anaerobic digestion of lipidic slaughterhouse waste.

Different inoculum to slaughterhouse waste (SHW) ratios (Ino/SHW) influences the digester performance, substrate utilization, and methane yield through microbial shift and their metabolic syntrophy. Acetoclastic Methanosarcina (68-87%) was dominant in the exponential phase, overpowering the initial abundance of Methanosaeta (86% of methanogens) in the SHW digesters. Positive interactions among acetogenic and acetate-oxidizing species of Clostridium (11%) with Methanosarcina (84% of methanogens) improved the methanogenic activity (292 mL g-1 VSinitial d-1) and final VS utilization (90%) at the highest Ino/SHW loading. In contrast, significant improvement of methane yield (152% higher than the control) at the lowest Ino/SHW loading was attributed to strong syntrophy among Methanosaeta (24% of methanogens) and its exoelectrogenic partners, Bythopirellula (0.52%) and Mariniphaga (0.08%) and the acetogenic Cloacimonas (0.16%) and Longilinea (0.32%). These syntrophic interactions among the core microbiota induced major metabolic activities, including butanoate, glycine, serine and threonine, methane, propanoate, and pyruvate metabolism, and quorum sensing.

Nutrient Enrichment Predominantly Affects Low Diversity Microbiomes in a Marine Trophic Symbiosis between Algal Farming Fish and Corals.

While studies show that nutrient pollution shifts reef trophic interactions between fish, macroalgae, and corals, we know less about how the microbiomes associated with these organisms react to such disturbances. To investigate how microbiome dynamics are affected during nutrient pollution, we exposed replicate Porites lobata corals colonized by the fish Stegastes nigricans, which farm an algal matrix on the coral, to a pulse of nutrient enrichment over a two-month period and examined the microbiome of each partner using 16S amplicon analysis. We found 51 amplicon sequence variants (ASVs) shared among the three hosts. Coral microbiomes had the lowest diversity with over 98% of the microbiome dominated by a single genus, Endozoicomonas. Fish and algal matrix microbiomes were ~20 to 70× more diverse and had higher evenness compared to the corals. The addition of nutrients significantly increased species richness and community variability between samples of coral microbiomes but not the fish or algal matrix microbiomes, demonstrating that coral microbiomes are less resistant to nutrient pollution than their trophic partners. Furthermore, the 51 common ASVs within the 3 hosts indicate microbes that may be shared or transmitted between these closely associated organisms, including Vibrionaceae bacteria, many of which can be pathogenic to corals.