Microbiome Patterns Research Articles

Study of the gut microbiome as a novel target for prevention of hospital-associated infections in intensive care unit patients.

Hospital-acquired infections (HAIs) are increasing due to the spread of multi-drugresistant organisms. Gut dysbiosis in an intensive care unit (ICU) patients at admission showed an altered abundance of some bacterial genera associated with the occurrence of HAIs and mortality. In the present study, we investigated the pattern of the gut microbiome in ICU patients at admission to correlate it with the development of HAIs during ICU stay. Twenty patients admitted to an ICU with a cross-matched control group of 30 healthy subjects of matched age and sex. Quantitative SYBR green real-time polymerase chain reaction was done for the identification and quantitation of selected bacteria. Out of those twenty patients, 35% developed ventilator-associated pneumonia during their ICU stay. Gut microbiome analysis showed a significant decrease in Firmicutes and Firmicutes to Bacteroidetes ratio in ICU patients in comparison to the control and in patients who developed HAIs in comparison to the control group and patients who did not develop HAIs. There was a statistically significant increase in Bacteroides in comparison to the control group. There was a statistically significant decrease in Bifidobacterium and Faecalibacterium prausnitzii and an increase in Lactobacilli in comparison to the control group with a negative correlation between Acute Physiology and Chronic Health Evaluation (APACHE) II score and Firmicutes to Bacteroidetes and Prevotella to Bacteroides ratios. Gut dysbiosis of patients at the time of admission highlights the importance of identification of the microbiome of patients admitted to the ICU as a target for preventing of HAIs.

Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection.

Sub-Saharan Africa has increased morbidity and mortality related to chronic obstructive pulmonary disease (COPD). COPD among people living with HIV (PLWH) has not been well studied in this region, where HIV/AIDS is endemic. Increasing evidence suggests that respiratory microbial composition plays a role in COPD severity. Therefore, we aimed to investigate microbiome patterns and associations among PLWH with COPD in Sub-Saharan Africa. We conducted a cross-sectional study of 200 adults stratified by HIV and COPD in rural Uganda. Induced sputum samples were collected as an easy-to-obtain proxy for the lower respiratory tract microbiota. We performed 16S rRNA gene sequencing and used PICRUSt2 (version 2.2.3) to infer the functional profiles of the microbial community. We used a statistical tool to detect changes in specific taxa that searches and adjusts for confounding factors such as antiretroviral therapy (ART), age, sex, and other participant characteristics. We could cluster the microbial community into three community types whose distribution was shown to be significantly impacted by HIV. Some genera, e.g., Veillonella, Actinomyces, Atopobium, and Filifactor, were significantly enriched in HIV-infected individuals, while the COPD status was significantly associated with Gammaproteobacteria and Selenomonas abundance. Furthermore, reduced bacterial richness and significant enrichment in Campylobacter were associated with HIV-COPD comorbidity. Functional prediction using PICRUSt2 revealed a significant depletion in glutamate degradation capacity pathways in HIV-positive patients. A comparison of our findings with an HIV cohort from the United Kingdom revealed significant differences in the sputum microbiome composition, irrespective of viral suppression. IMPORTANCE Even with ART available, HIV-infected individuals are at high risk of suffering comorbidities, as shown by the high prevalence of noninfectious lung diseases in the HIV population. Recent studies have suggested a role for the respiratory microbiota in driving chronic lung inflammation. The respiratory microbiota was significantly altered among PLWH, with disease persisting up to 3 years post-ART initiation and HIV suppression. The community structure and diversity of the sputum microbiota in COPD are associated with disease severity and clinical outcomes, both in stable COPD and during exacerbations. Therefore, a better understanding of the sputum microbiome among PLWH could improve COPD prognostic and risk stratification strategies. In this study, we observed that in a virologically suppressed HIV cohort in rural Uganda, we could show differences in sputum microbiota stratified by HIV and COPD, reduced bacterial richness, and significant enrichment in Campylobacter associated with HIV-COPD comorbidity.

Integration of Transcriptomics and Microbiomics Reveals the Responses of Bellamya aeruginosa to Toxic Cyanobacteria.

Frequent outbreaks of harmful cyanobacterial blooms and the cyanotoxins they produce not only seriously jeopardize the health of freshwater ecosystems but also directly affect the survival of aquatic organisms. In this study, the dynamic characteristics and response patterns of transcriptomes and gut microbiomes in gastropod Bellamya aeruginosa were investigated to explore the underlying response mechanisms to toxic cyanobacterial exposure. The results showed that toxic cyanobacteria exposure induced overall hepatopancreatic transcriptome changes. A total of 2128 differentially expressed genes were identified at different exposure stages, which were mainly related to antioxidation, immunity, and metabolism of energy substances. In the early phase (the first 7 days of exposure), the immune system may notably be the primary means of resistance to toxin stress, and it performs apoptosis to kill damaged cells. In the later phase (the last 7 days of exposure), oxidative stress and the degradation activities of exogenous substances play a dominant role, and nutrient substance metabolism provides energy to the body throughout the process. Microbiomic analysis showed that toxic cyanobacteria increased the diversity of gut microbiota, enhanced interactions between gut microbiota, and altered microbiota function. In addition, the changes in gut microbiota were correlated with the expression levels of antioxidant-, immune-, metabolic-related differentially expressed genes. These results provide a comprehensive understanding of gastropods and intestinal microbiota response to toxic cyanobacterial stress.

P928 Identification of mucosal microbiome-host gene interactions in ulcerative colitis patients

Abstract Background With the development of NGS analysis, many studies have been performed on the role of gut microbiota in the pathogenesis of inflammatory bowel disease and the possibility of gut bacteria as a diagnosis and treatment modality for IBD. However, the role of gut microbiota in clinical applications such as markers for diagnosis, prognosis prediction and the therapeutic agents is still unclear, and further studies on host-microbe interactions are still needed. In this study, we tried to detect mucosal bacterial species which can discriminate between ulcerative colitis and normal control and the correlations between the microbiome and gene expression through integrated analysis of metagenomic sequencing and RNA-sequencing in the colonic mucosa of UC patients and normal controls. Methods Colonic tissues obtained from UC patients (n = 7) and normal control (n = 13) were subjected to 16S rRNA sequencing of the microbiome and next-generation sequencing (NGS) RNA-seq. The differentially expressed genes (DEGs) and DEGs-based enrichment terms were obtained. Gene set enrichment analysis (GSEA) and PathfindR were also used to reveal significant differences of meaningful gene sets. The datasets were analyzed individually and integrated including sociomedical factors for combined analysis using bioinformatics approaches. Correlation analyses were performed between microbiome and gene expression and network analysis were presented. Results From DEG results, 28 and 18 genes were higher expressed in the UC and normal groups, respectively. GSEA provided total 1,857 gene sets enriched in the UC group. We identified that patients with UC show decreased species such as Bacteroides coprocola, Bacteroides phlebeius, Parabacteroides merdae and increased abundance of other species, such as Eubacterium._eligens, Clostridium_clostridioforme, Faecalibacterium_prausnitzii. An integrative analysis identified immunomodulatory genes including HLA-G, PSMA4 for which gene expression is negatively correlated with Bacteroides species. Conclusion In addition to identifying mucosal microbiome and host-genes expression patterns in the UC patients, we showed the potential role of host-microbe interactions in the development of UC. These findings provided the integrated analysis of microbe- host gene can be served as a biomarker for diagnosis and treatment target in patients with UC.

P266 Potential oral microbial markers for differential diagnosis of Crohn’s disease and ulcerative colitis using machine learning model

Abstract Background Although the gut microbiome dysbiosis have independently been shown to be associated with inflammatory bowel disease (IBD), less is known about the relationship between oral microbiota and IBD. This study aimed to elucidate unique microbiome patterns in saliva from patients with IBD and investigate potential oral microbial markers for differentiating Crohn’s disease (CD) and ulcerative colitis (UC). Methods A multicenter, prospective cohort study recruited patients with IBD (UC, n=175, CD, n=127) and unrelated healthy controls (HC, n=100) to examine microbiota within the oral microenvironments. We used 16S rRNA gene sequencing data as features in training machine learning models (sPLS-DA, Sparse Partial Least-Squares Discriminant Analysis) to classify CD and UC. Results The V3-V4 amplicon reads of the saliva 16S rRNA sequencing data were taxonomically classified to a total of 2839 taxa (2270 genera) using Kraken2 based on Silva 138.1 reference. The sequences that were not classifiable down to family level were removed, and the samples having sequence depth less than 30000 were also removed, resulting in 2616 taxa for 390 samples (UC, n=168, CD, n=124, HC, n=98). The alpha diversity analysis revealed that the microbiome in IBD patients were significantly less rich than the healthy controls, while CD samples were slightly richer then UC samples (Figure 1, Observed, P = 0.01, Shannon index, p=0.02, Chao index, P=0.0001). An sPLS-DA model with 470 taxa as features was able to distinguish IBD vs control with high performance (AUROC=0.9774), while a separate sPLS-DA model with 130 features classified CD vs UC with an AUROC of 0.8755 (Figure 2,3). Conclusion Collectively, oral microbial profiles can serve as a diagnostic marker to discriminate patients with IBD from HC, and patients with CD from UC. As obtaining oral samples is relatively easier than obtaining stool or intestinal biopsies, an opportunity exists to perform oral microbiome-based studies in larger cohort sizes, preferentially in a longitudinal fashion.

Distinct response patterns of plants and soil microorganisms to agronomic practices and seasonal variation in a floodplain ecosystem.

Climate change and anthropogenic activities are the greatest threats to floodplain ecosystems. A growing body of literature shows that floodplain ecosystems have experienced increased chemical fertilizer and pesticide loads, which will disturb the above and belowground ecosystems. However, we lack knowledge regarding the effects of such human activities on the vegetation and soil microbiomes in these ecosystems. In the present study, plant functional traits and Illumina Mi-Seq sequencing were to assess the impact of nitrogen fertilizer and glyphosate addition on the structure and function of the vegetation and soil microbiomes (bacteria, fungi, and protists) in a floodplain ecosystem, and to assess the influence of seasonal variation. We identified distinct response mechanisms of plant and microbial communities to the addition of nitrogen fertilizer and glyphosate, and seasonal variation. Nitrogen fertilizer and glyphosate significantly affected plant diversity, aboveground and underground biomass, and C and N content and significantly changed the leaf area and plant stature of dominant plants. However, the addition of nitrogen fertilizer and glyphosate did not significantly affect the diversity and structure of bacterial, fungal, and protist communities. The application of nitrogen fertilizer could improve the negative effects of glyphosate on the functional traits of plant communities. The seasonal variation of floodplain has significantly changed the soil's physical, chemical, and biological properties. Our results showed that compared with that in summer, the soil ecosystem multifunctionality of the floodplain ecosystem in autumn was significantly lower. Seasonal variation had a significant effect on plant diversity and functional traits. Moreover, seasonal variation significantly affected the community compositions, diversity, and structure of bacteria, fungi, and protists. Seasonal variation had a stronger impact on fungal community assembly than on that of bacteria and protists. In summer, the assembly of the fungal community was dominated by a deterministic process, while in autumn, it is dominated by a stochastic process. In addition, the negative association among bacteria, fungi, and protists has been strengthened in autumn and formed a more robust network to cope with external changes. These results extended our understanding of the ecological patterns of soil microbiomes in floodplain ecosystems and provided support for enhancing the ecological barrier function and the service potential of floodplain ecosystems.

Comparative analysis of microbiome indicators in patients with mental disorders and in healthy volunteers

The state of human microbiome is closely related to higher nervous activity. Studies of the relationship between the state of the microbiome and the formation of neuropsychiatric disorders represent a very promising field of research. This work presents the results of a comparative analysis of the profiles of microbiome indicators in 36 ± 12-year-old patients with mental and behavioral disorders (n = 30) and in healthy volunteers (n = 10). The profiles of microbiome indicators were measured on the basis of blood analysis by mass chromatospectrometry. Numerous significant differences were found in microbiome patterns between patients and controls. On the basis of the established differences, two point scales were proposed and verified, which can be regarded as a kind of indices of “psychopathogenicity of the microbiome”. These scales make it possible not only to distinguish patients from controls, but also to rank the subjects according to the degree of “psychopathogenicity” of the microbiome profile.

The oral cancer microbiome contains tumor space-specific and clinicopathology-specific bacteria.

The crosstalk between the oral microbiome and oral cancer has yet to be characterized. This study recruited 218 patients for clinicopathological data analysis. Multiple types of specimens were collected from 27 patients for 16S rRNA gene sequencing, including 26 saliva, 16 swabs from the surface of tumor tissues, 16 adjacent normal tissues, 22 tumor outer tissue, 22 tumor inner tissues, and 10 lymph nodes. Clinicopathological data showed that the pathogenic bacteria could be frequently detected in the oral cavity of oral cancer patients, which was positively related to diabetes, later T stage of the tumor, and the presence of cervical lymphatic metastasis. Sequencing data revealed that compared with adjacent normal tissues, the microbiome of outer tumor tissues had a greater alpha diversity, with a larger proportion of Fusobacterium, Prevotella, and Porphyromonas, while a smaller proportion of Streptococcus. The space-specific microbiome, comparing outer tumor tissues with inner tumor tissues, suggested minor differences in diversity. However, Fusobacterium, Neisseria, Porphyromonas, and Alloprevotella were more abundant in outer tumor tissues, while Prevotella, Selenomonas, and Parvimonas were enriched in inner tumor tissues. Clinicopathology-specific microbiome analysis found that the diversity was markedly different between negative and positive extranodal extensions, whereas the diversity between different T-stages and N-stages was slightly different. Gemella and Bacillales were enriched in T1/T2-stage patients and the non-lymphatic metastasis group, while Spirochaetae and Flavobacteriia were enriched in the extranodal extension negative group. Taken together, high-throughput DNA sequencing in combination with clinicopathological features facilitated us to characterize special patterns of oral tumor microbiome in different disease developmental stages.

Recovery patterns of the coral microbiome after relief of algal contact

Interactions between macroalgae and corals are omnipresent on eutrophied and overfished reefs worldwide. Contact with macroalgae can disrupt corals and their microbiomes through diverse mechanisms, including shading, abrasion, and the release of algal exudates. However, changes in the coral microbiome after algal contact ceases have not been studied. We investigated the recovery of the microbiome of massive reef-building Porites corals following experimental removal of the overgrowing green macroalga Halimeda macrophysa. We followed changes in the microbiome of macroalgal-removed and adjacent healthy-looking tissue of coral colonies over 40 days. Coral tissue was predominantly bleached underneath the macroalgae but regained almost its full pigmentation by day 40. Despite this recovery in pigmentation, the bacterial microbiome of macroalgal-removed coral tissue did not return to that of adjacent healthy-looking tissue (control). Overall, macroalgal contact led to the suppression of Gammaproteobacteria and increased diversity and dominance of Alphaproteobacteria, a shift that persevered for 40 days after algal removal. Causal effect analysis showed a positive effect of influential OTUs in healthy-looking tissue assigned to Gammaproteobacteria and Bacteroidia on the relative abundance of other OTUs within these classes. The effect of influential OTUs assigned to Alphaproteobacteria in macroalgal-removed tissue on the relative abundance of other OTUs was more diverse. Despite the high heterogeneity of coral microbiomes, differences in the relative abundance of main bacterial classes and orders between control/healthy and macroalgal-removed tissue showed temporal patterns. Differences in the Alpha-, Gamma-, Deltaproteobacteria and Bacteroidia between control/healthy and macroalgal-removed tissue increased after cessation of macroalga contact and stabilized or declined towards day 40. Acidimicrobiia, Deltaproteobacteria, Rhodospirillales and Rhodovibrionales returned to average relative abundances in the adjacent control/healthy tissue after 40 days. Nevertheless, Rhizobiales and Rhodobacterales (Alphaproteobacteria) still dominated the macroalgal-removed microbiome on day 40. We conclude that macroalgal overgrowth induces changes in the coral microbiome, and that algal removal did not lead to full recovery of the microbiome in 40 days. Return of pigmentation and distinct shifts in bacterial groups over time appear a possible pathway to the recovery of the coral microbiome after macroalgal removal.

Metabarcoding reveals the differential sensitivity of planktonic microbiome to environmental filtering and biointeraction in Sansha Yongle blue hole

The Sansha Yongle blue hole (SYBH) is the world’s deepest blue hole known so far and its unique hydrochemical characteristics make it a valuable site for studying biodiversity and ecological processes. Here, we used metabarcoding approach to investigate the diversity, assembly mechanism and co-occurrence pattern of planktonic microbiome in SYBH. Our results revealed the distinct separation of communities from upper oxic, middle oxic and suboxic-anoxic layer and significant day-night difference was detected in the upper-layer community of microeukaryotes, indicating potential diel migration. Stochastic processes played a significant role in the community assembly of microeukaryotes, while deterministic processes dominated in prokaryotes, confirming the stronger environmental filtering on prokaryotes as also suggested by the correlation with environmental variables. Microeukaryotes were less sensitive to environments but significantly affected by cross-domain biointeraction. When comparing the subcommunities of different abundance, we found that abundant taxa were widespread while rare taxa were habitat-specific. In co-occurrence network, over 87% of the interactions and 19 out of 20 keystone OTUs (Operational Taxonomic Units) were affiliated to moderate or rare taxa, suggesting the importance of non-abundant taxa in maintaining community stability. The predominant positive edges in the network pointed to that interspecies cooperation may be one of the ecological strategies in SYBH. Overall, we highlight the divergent assembly pattern and different driving forces in shaping plankton microbiome in SYBH, which may advance current understanding on diversity and dynamics of marine life in blue hole ecosystems.

Snapshot into the Type-2-Diabetes-Associated Microbiome of a Romanian Cohort

The prevalence of type 2 diabetes mellitus (T2D) is alarmingly increasing worldwide, urgently calling for a better understanding of the underlying mechanisms in order to step up prevention and improve therapeutic approaches. It is becoming evident that the gut microbiota seem to have an endless capacity to impact T2D. In this study, we profile the gut microbiome patterns in T2D patients from Romania, by using quantitative Real-Time PCR and next generation sequencing. We enrolled a total of 150 individuals (105 T2D patients, 50 of them without metformin treatment and 45 healthy volunteers). The levels of potentially beneficial butyrate-producing bacteria were significantly reduced, while potentially pathogenic microorganisms such as Enterobacteriaceae and Fusobacterium were enriched in T2D patients. We evaluated the correlation between clinical parameters and gut microbiota and identified the genera Bacteroides, Alistipes, Dialister, Bilophila and Sutterella as possible detrimental factors in T2D. Our findings suggest that the gut microbiota may be a potential target in novel approaches to halt the development of T2D-associated complications.

Probiotic Therapy with Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis Results in Infarct Size Limitation in Rats with Obesity and Chemically Induced Colitis

In this study, we investigated the effect of three different probiotics, namely, a combination of Lactobacillus acidophilus (LA-5) and Bifidobacterium animalis subsp. lactis (BB-12), Saccharomyces boulardii, and Enterococcus faecium L3 on myocardial infarct size in rats with diet-induced obesity (DIO) and chemically-induced colitis (CIC). Potential associations between the effects of probiotics on myocardial ischemia-reperfusion injury and gut microbiome patterns as well as the serum levels of pro- and anti-inflammatory cytokines, lipopolysaccharide, and short chain fatty acids were also studied. Intragastric administration of lyophilized Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis at a dose of 1.2 × 108 CFU/mL for 15 days resulted in myocardial infarct size reduction in rats with DIO, CIC, and antibiotic-induced dysbiosis. This cardioprotective effect was associated with specific changes in cytokine concentrations, namely reduced levels of IL-1β, TNF-α, IL-2, and IL-8. At the same time, the use of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis was accompanied by a significant reduction in lipopolysaccharide level, suggesting normalization of intestinal epithelial barrier permeability. However, the cardioprotective effect of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis is not secondary to improved healing of the intestinal mucosa in CIC, as evidenced by the lack of difference in histopathological scores.

Carbon source utilization pattern of soil bacterial microbiome of bambara groundnut rhizosphere at the different growth stages determines soil fertility

The diversity of microbes in the soil of plants is important for sustainable agriculture as these microbes are important in carrying out different functional processes to improve the soil and invariably plant growth. Inversely the presence of the crop also affects the types of microbial communities in the soil. In this study, bambara groundnut was grown during the planting season in South Africa, from November to March 2014/2015 and 2015/2016 and soil samples were taken after every 4 weeks after planting. Soil samples were taken 15 cm deep from 2 different landraces named VBR and VL. Microbial diversity was determined by soil microbial Carbon Source Utilization Profiles (CSUP) using BIOLOG™ GN2 plates. The abundance and richness of the soil microbes was also determined using the Shannon-Weaver and Evenness diversity indices. The diversity of the soil microbial population changed over the stages of plant growth, according to cluster analysis. Bacterial abundance and diversity were higher at 4 and 8 weeks after planting (WAP). The microbial abundance (richness index) in this study ranged from 0.64 to 0.94 with cultivar VL2 at 8 WAP being the highest while bulk soil (control), R2 was the lowest. The Shannon-Weaver index varied between 2.19 and 4.00 with the lowest corresponding to control while the highest was VL2 at 8 WAP. Carbon sources utilized by bacterial communities spread across the 96 carbon sources. The highest utilization of carboxylic acids, ester, amino acids and polymers and carbohydrates was found in the bacterial communities of the different landraces across growth stages. The highest utilization of alcohols, amides, amines, aromatic chemicals, brominated chemicals and phosphorylated chemicals was found in the control landraces. This indicates that the soil samples between 4 WAP and 12 WAP were richer in diversity of microbial species and their abundance. This soil diversity and richness is an indicator of the quality of the soil in order to increase crop yields and agricultural production.

Characterization of longitudinal nasopharyngeal microbiome patterns in maternally HIV-exposed Zambian infants

Background: Previous studies of infants born to HIV-positive mothers have linked HIV exposure to poor outcomes from gastrointestinal and respiratory illnesses, and to overall increased mortality rates. The mechanism behind this is unknown, but it is possible that differences in the nasopharyngeal (NP) microbiome between HIV-unexposed and HIV-exposed infants could play a role in perpetuating some outcomes. Methods: We conducted a longitudinal analysis of 170 NP swabs of healthy HIV-exposed, uninfected (HEU; n=10) infants and their HIV(+) mothers and HIV-unexposed, uninfected (HUU; n=10) infants and their HIV(-) mothers. These swabs were identified from a sample library collected in Lusaka, Zambia between 2015 and 2016. Using 16S rRNA gene sequencing, we characterized the maturation of the microbiome over the first 14 weeks of life to determine what quantifiable differences exist between HEU and HUU infants, and what patterns are reflected in the mothers' NP microbiomes. Results: In both HEU and HUU infants, Staphylococcus and Corynebacterium began as primary colonizers of the NP microbiome but were in time replaced by Dolosigranulum, Streptococcus, Moraxella and Haemophilus. When studying differences between infants, the microbe Staphylococcus haemolyticus indicated a distinctive high association with HIV exposure at birth, even when accounting for the interaction between HIV exposure status and time of sampling. When comparing infants to their mothers with paired analyses, HEU infants’ NP microbiome composition was only slightly different from their HIV(+) mothers at birth or 14 weeks, including in their carriage of S. pneumoniae, H. influenzae, and S. haemolyticus. Conclusions: Our analyses indicate that the HEU infants in our study exhibit subtle differences in the NP microbial composition throughout the sampling interval. Given our results and the sampling limitations of our study, we believe that further research must be conducted in order to confidently understand the relationship between HIV exposure and infants’ NP microbiomes.

Sex-specific gut microbiome profiles among preterm infants during the neonatal intensive care hospitalization.

The gut microbiota among preterm infants is shaped by sex and feeding types. However, sex-specific weekly patterns of gut microbiome profiles among preterm infants during their neonatal intensive care unit (NICU) hospitalization remain unclear. This study aimed to investigate the effect of sex on the weekly development of preterm neonatal gut microbiota in the first 4 weeks of NICU hospitalization. This secondary data analysis included 28 preterm neonates with 261 stool samples collected from January 2014 to February 2015 in the Northeastern United States. The 16S rRNA V4 gene regions of the stool samples were sequenced and aligned against the SILVA 132 database by using Mothur 1.42.3. The sex-specific weekly diversity indexes and relative abundance of bacterial taxonomic composition were generated by Mothur and analyzed by R packages. Sex-specific weekly compositional patterns of the gut microbiome and predicted metabolic functions of gut microbiome profiles were compared, respectively. In each week of the NICU hospitalization, preterm females and males had significantly distinguished β-diversity indices and compositions of gut microbiota. Both females and males had significantly enriched Bifidobacterium, a protection feature, in stool samples collected in the third week compared with those in the second week. The predicted metabolic pathways were significantly different between females and males in the second, third, and fourth week of the NICU hospitalization. Both females and males had significantly abundant pathways. Males consistently had more abundance of "lipopolysaccharide biosynthesis" than females in the second, third, and fourth week. Males also had a significant abundance of "membrane and intracellular structural molecules" and "glycan biosynthesis and metabolism" in the second and third week. Sex shaped the weekly patterns of preterm neonatal gut microbiome profiles during the first 4 weeks of the NICU hospitalization. Further clinical interventions should consider the distinct gut microbiota compositions and predicted functional profiles between female and male preterm neonates.

Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments.

Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for <1 year in duration and scheduled for release; Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients.

Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea)

Because of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules—and taxa—were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance.

Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale.

Microbial communities in the rhizosphere play a crucial role in determining plant growth and crop yield. A few studies have been performed to evaluate the diversity and co-occurrence patterns of rhizosphere microbiomes in soybean (Glycine max) at a regional scale. Here, we used a culture-independent method to compare the bacterial communities of the soybean rhizosphere between Nebraska (NE), a high-yield state, and Oklahoma (OK), a low-yield state. It is well known that the rhizosphere microbiome is a subset of microbes that ultimately get colonized by microbial communities from the surrounding bulk soil. Therefore, we hypothesized that differences in the soybean yield are attributed to the variations in the rhizosphere microbes at taxonomic, functional, and community levels. In addition, soil physicochemical properties were also evaluated from each sampling site for comparative study. Our result showed that distinct clusters were formed between NE and OK in terms of their soil physicochemical property. Among 3 primary nutrients (i.e., nitrogen, phosphorus, and potassium), potassium is more positively correlated with the high-yield state NE samples. We also attempted to identify keystone communities that significantly affected the soybean yield using co-occurrence network patterns. Network analysis revealed that communities formed distinct clusters in which members of modules having significantly positive correlations with the soybean yield were more abundant in NE than OK. In addition, we identified the most influential bacteria for the soybean yield in the identified modules. For instance, included are class Anaerolineae, family Micromonosporaceae, genus Plantomyces, and genus Nitrospira in the most complex module (ME9) and genus Rhizobium in ME23. This research would help to further identify a way to increase soybean yield in low-yield states in the U.S. as well as worldwide by reconstructing the microbial communities in the rhizosphere.

Machine Learning and Canine Chronic Enteropathies: A New Approach to Investigate FMT Effects.

Simple SummaryFecal microbiota transplantation (FMT) represents a very promising approach to decrease disease activity in chronic enteropathies (CE). Although CE and dysbiosis are undoubtedly connected, the relationship between remission mechanisms and microbiome changes has not been elucidated yet. Indeed, CE is a heterogeneous disease consisting of many different subtypes, and the dynamic of the microbial community is very complex. The aim of this study was to report the clinical effects of oral freeze-dried FMT in dogs affected by CE, analyzing the fecal microbiome before and after FMT, and comparing the microbial composition with a healthy population. Artificial intelligence algorithms were applied to address the high complexity of microbiomes. Clinical signs of improvement were observed in three-quarters of receivers, proving the effectiveness of the treatment in the freeze-dried form. Machine learning algorithms successfully predicted healthy and diseased animal categories, using microbial compositions. Every receiver showed microbiome variation after the transplant, but there was high heterogeneity in the response. These findings are the first step for further research on a larger dataset that could identify different healing patterns of microbiome changes.Fecal microbiota transplantation (FMT) represents a very promising approach to decreasing disease activity in canine chronic enteropathies (CE). However, the relationship between remission mechanisms and microbiome changes has not been elucidated yet. The main objective of this study was to report the clinical effects of oral freeze-dried FMT in CE dogs, comparing the fecal microbiomes of three groups: pre-FMT CE-affected dogs, post-FMT dogs, and healthy dogs. Diversity analysis, differential abundance analysis, and machine learning algorithms were applied to investigate the differences in microbiome composition between healthy and pre-FMT samples, while Canine Chronic Enteropathy Clinical Activity Index (CCECAI) changes and microbial diversity metrics were used to evaluate FMT effects. In the healthy/pre-FMT comparison, significant differences were noted in alpha and beta diversity and a list of differentially abundant taxa was identified, while machine learning algorithms predicted sample categories with 0.97 (random forest) and 0.87 (sPLS-DA) accuracy. Clinical signs of improvement were observed in 74% (20/27) of CE-affected dogs, together with a statistically significant decrease in CCECAI (median value from 5 to 2 median). Alpha and beta diversity variations between pre- and post-FMT were observed for each receiver, with a high heterogeneity in the response. This highlighted the necessity for further research on a larger dataset that could identify different healing patterns of microbiome changes.

Got milk? Maternal immune activation during the mid-lactational period affects nutritional milk quality and adolescent offspring sensory processing in male and female rats.

Previous studies have underscored the importance of breastfeeding and parental care on offspring development and behavior. However, their contribution as dynamic variables in animal models of early life stress are often overlooked. In the present study, we investigated how lipopolysaccharide (LPS)-induced maternal immune activation (MIA) on postnatal day (P)10 affects maternal care, milk, and offspring development. MIA was associated with elevated milk corticosterone concentrations on P10, which recovered by P11. In contrast, both milk triglyceride and percent creamatocrit values demonstrated a prolonged decrease following inflammatory challenge. Adolescent MIA offspring were heavier, which is often suggestive of poor early life nutrition. While MIA did not decrease maternal care quality, there was a significant compensatory increase in maternal licking and grooming the day following inflammatory challenge. However, this did not protect against disrupted neonatal huddling or later-life alterations in sensorimotor gating, conditioned fear, mechanical allodynia, or reductions in hippocampal parvalbumin expression in MIA offspring. MIA-associated changes in brain and behavior were likely driven by differences in milk nutritional values and not by direct exposure to LPS or inflammatory molecules as neither LPS binding protein nor interleukin-6 milk levels differed between groups. These findings reflected comparable microbiome and transcriptomic patterns at the genome-wide level. Animal models of early life stress can impact both parents and their offspring. One mechanism that can mediate the effects of such stressors is changes to maternal lactation quality which our data show can confer multifaceted and compounding effects on offspring physiology and behavior.