SCNIC: Sparse correlation network investigation for compositional data

Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers

Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL-1) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.

Distinguishing critical microbial community shifts from normal temporal variability in human and environmental ecosystems

Differentiating significant microbial community changes from normal fluctuations is vital for understanding microbial dynamics in human and environmental ecosystems. This knowledge could enable early warning systems to monitor critical changes affecting human or environmental health. We applied 16S rRNA gene sequencing and time-series analysis to model bacterial abundance trajectories in human gut and wastewater microbiomes. We evaluated various model architectures using datasets from two human studies and five wastewater settings. Long short-term memory (LSTM) models consistently outperformed other models in predicting bacterial abundances and detecting outliers, as measured by multiple metrics. Prediction intervals for each genus allowed us to identify significant changes and signaling shifts in community states. This study proposes a machine learning model capable of monitoring microbial communities and providing insights into their responses to internal and external factors in medical and environmental settings.

Community dynamics during de novo colonization of the nascent peri-implant sulcus

Dental implants have restored masticatory function to over 100 000 000 individuals, yet almost 1 000 000 implants fail each year due to peri-implantitis, a disease triggered by peri-implant microbial dysbiosis. Our ability to prevent and treat peri-implantitis is hampered by a paucity of knowledge of how these biomes are acquired and the factors that engender normobiosis. Therefore, we combined a 3-month interventional study of 15 systemically and periodontally healthy adults with whole genome sequencing, fine-scale enumeration and graph theoretics to interrogate colonization dynamics in the pristine peri-implant sulcus. We discovered that colonization trajectories of implants differ substantially from adjoining teeth in acquisition of new members and development of functional synergies. Source-tracking algorithms revealed that this niche is initially seeded by bacteria trapped within the coverscrew chamber during implant placement. These pioneer species stably colonize the microbiome and exert a sustained influence on the ecosystem by serving as anchors of influential hubs and by providing functions that enable cell replication and biofilm maturation. Unlike the periodontal microbiome, recruitment of new members to the peri-implant community occurs on nepotistic principles. Maturation is accompanied by a progressive increase in anaerobiosis, however, the predominant functionalities are oxygen-dependent over the 12-weeks. The peri-implant community is easily perturbed following crown placement, but demonstrates remarkable resilience; returning to pre-perturbation states within three weeks. This study highlights important differences in the development of the periodontal and peri-implant ecosystems, and signposts the importance of placing implants in periodontally healthy individuals or following the successful resolution of periodontal disease.

Age-related dynamics of predominant methanogenic archaea in the human gut microbiome

BACKGROUND

The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.

METHODS

Shotgun metagenomic data from the stool samples of young adults (n = 127, Age: 19-59 y), older adults (n = 86, Age: 60-99 y), and centenarians (n = 34, age: 100-109 years) were analyzed.

RESULTS

Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.

CONCLUSIONS

This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.

Discovering the dynamics of peach fruit mycobiome throughout fruit development season by high-throughput sequencing

The mycobiome is comprised of a rich array of fungal species that compete for resources, and species diversity and prevalence exhibit a dynamic structure under the influence of many factors. While the host fruit develops, the prevalence and the arrangement of fungal species in this mycobiome also change, forming a dynamic microenvironment. In this study, fungal diversity on peach fruit surfaces at different developmental stages have been determined to better understand the changes in fungal diversity and disease occurrence by using metabarcoding of the full ITS region and processing the obtained high-throughput sequencing data with various bioinformatic analyses. It has been found that fungal diversity in early developmental stages is higher, and the diversity declines as the fruit matures, likely due to more prevalent fungal species establishing themselves on the surface as the fruit develops. Additionally, this research reveals that the prevalence of pathogens does not necessarily mean that disease will develop, as pathogenic species were found to be at higher prevalence percentages when compared to non-pathogenic species in healthy fruit samples. This study also identified the Monilinia polystroma species at a molecular level for the first time in Türkiye; however, no symptomatic signals were recorded on the host. The study provides valuable data for mycobiome studies, while also highlighting its importance in optimizing sustainable disease management strategies.

Protective effects of Mycobacterium vaccae ATCC 15483 against "Western"-style diet-induced weight gain and visceral adiposity in adolescent male mice

The prevalence of noncommunicable inflammatory disease is increasing in modern urban societies, posing significant challenges to public health. Novel prevention and therapeutic strategies are needed to effectively deal with this issue. One promising approach is leveraging microorganisms such as Mycobacterium vaccae ATCC 15483, known for its anti-inflammatory, immunoregulatory, and stress-resilience properties. This study aimed to assess whether weekly subcutaneous administrations of a whole-cell, heat-killed preparation of M. vaccae ATCC 15483 (eleven injections initiated one week before the onset of the diet intervention), relative to vehicle injections, in adolescent male C57BL/6N mice can mitigate inflammation associated with Western-style diet-induced obesity, which is considered a risk factor for a number of metabolic and inflammatory diseases. Our results show that treatment with M. vaccae ATCC 15483 prevented Western-style diet-induced excessive weight gain, visceral adipose tissue accumulation, and elevated plasma leptin concentrations. The Western-style diet, relative to a control diet condition, decreased alpha diversity and altered the community composition of the gut microbiome, increasing the Bacillota to Bacteroidota ratio (formerly referred to as the Firmicutes to Bacteroidetes ratio). Despite the finding that M. vaccae ATCC 15483 prevented Western-style diet-induced excessive weight gain, visceral adipose tissue accumulation, and elevated plasma leptin concentrations, it had no effect on the diversity or community composition of the gut microbiome, suggesting that it acts downstream of the gut microbiome to alter immunometabolic signaling. M. vaccae ATCC 15483 reduced baseline levels of biomarkers of hippocampal neuroinflammation and microglial priming, such as Nfkbia and Nlrp3, and notably decreased anxiety-like defensive behavioral responses. The current findings provide compelling evidence supporting the potential for M. vaccae ATCC 15483 as a promising intervention for prevention or treatment of adverse immunometabolic outcomes linked to the consumption of a Western-style diet and the associated dysbiosis of the gut microbiome.

Microbiome Analysis of Area in Proximity to White Spot Lesions Reveals More Harmful Plant Pathogens in Maize

Plant microbiomes play a major role in plant health, growth, and development, enhancing resistance to pathogen invasion. However, despite the extensive research on the phyllosphere microbiome, it remains unclear how the microbiome of leaves in proximity to diseased leaves responds to pathogen invasion. We investigate the response of the maize phyllosphere microbiome to maize white spot by assessing the microbiome dynamics associated with the white spot portion and the area in proximity using 16S and ITS high-throughput sequencing analysis. Our results showed that the bacterial diversities were higher in the diseased portion and area in proximity to the spot than those in healthy plants. At the same time, lower fungal diversity was recorded in the diseased portion compared to portions in proximity to it and healthy leaves. The spot portion had a significant influence on the microbial composition. The diseased portion, the area in proximity to it, and the healthy leaves were dominated by the bacterial genera Sphingomonas, Delftia, Chryseobacterium, Stenotrophomonas, Methylobacterium-methylorubrum, and Bacteroides. Still, the abundance of Sphingomonas decreased in the healthy leaves with a corresponding increase in Stenotrophomonas. Conversely, the fungal genus Setophoma dominated the diseased portion, while the fungal pathogens Cladosporium, Alternaria, and Exserohilum were highly abundant in the samples from the area in proximity to it. In addition, a co-occurrence network analysis revealed a complex fungal network in healthy leaves and those in proximity to leaves infected with white spot compared to the diseased portion. This study suggests that the area in proximity to the maize leaf infected with white spot disease is colonized by more harmful plant pathogenic fungi for disease progression.

Topology of gut Microbiota Network and Guild-Based Analysis in Chinese Adults

Gut microbiota with co-abundant behaviors is considered belonging to the same guild in micro-ecosystem. In this study, we established co-abundance networks of operational taxonomic units (OTUs) among 2944 Chinese adults from the Shanghai Men's and Women's Health Studies and observed a positive connection-dominated scale-free network using Sparse Correlations for Compositional data (SparCC). The closeness centrality was negatively correlated with other degree-based topological metrics in the network, indicating the isolated modularization of the bacteria. A total of 130 guilds were constructed, with a high modularity of 0.68, and retaining more diversity of OTUs than genus classification. The scores of guild structure similarity for comparisons between all, the healthy and the unhealthy subjects were higher than those derived from randomized permutations, suggesting a robust guild structure. We further used the constructed 130 guilds as the aggregation units to identify gut microbiota that may be associated with type 2 diabetes, and found that the OTUs in 21 significant guilds relevant to diabetes belonged to 19 of 41 (46.3%) previously reported genera (derived from Disbiome database), while only 10 (24.4%) showed different abundances between diabetes patients and healthy subjects in genus-based analysis. Our study reveals modularization of gut microbiota as guilds in Chinese populations, and demonstrates advantages of guild-based analysis in identifying diabetes-related gut bacteria. The analytical method based on microbial networks should be widely used to deepen our understanding of the role of gut microbiota in human health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-024-00211-8.

First-year dynamics of the anaerobic microbiome and archaeome in infants' oral and gastrointestinal systems

Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants (n = 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in Streptococcus and the emergence of anaerobic genera such as Granulicatella. This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1-3) than in BF infants (months 4-6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with Methanobrevibacter being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants' GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.

IMPORTANCE

The first year of life is a crucial period for establishing a healthy human microbiome. Our study analyses the role of archaea and obligate anaerobes in the development of the human oral and gut microbiome, with a specific focus on the impact of breastfeeding in this process. Our findings demonstrated that the oral and gut microbiomes of breastfed infants undergo distinct phases of increased dynamics within the first year of life. In contrast, the microbiomes of non-breastfed infants are more mature from the first month, leading to a steadier development without distinct transitional phases in the first year. Additionally, we found that archaeal signatures are present in infants under 1 year of age, but they do not form a stable archaeome. In contrast to this, we could track specific bacterial strains transitioning from oral to gut or persisting in the gut over time.

Phylosymbiosis and Elevated Cancer Risk in Genetically Depauperate Channel Island Foxes

Examination of the host-associated microbiome in wildlife can provide critical insights into the eco-evolutionary factors driving species diversification and response to disease. This is particularly relevant for isolated populations lacking genomic variation, a phenomenon that is increasingly common as human activities create habitat 'islands' for wildlife. Here, we characterised the gut and otic microbial communities of one such species: Channel Island foxes (Urocyon littoralis). The gut microbiome provided evidence of phylosymbiosis by reflecting the host phylogeny, geographic proximity, history of island colonisation and contemporary ecological differences, whereas the otic microbiome primarily reflected geography and disease. Santa Catalina Island foxes are uniquely predisposed to ceruminous gland tumours following infection with Otodectes cynotis ear mites, while San Clemente and San Nicolas Island foxes exhibit ear mite infections without evidence of tumours. Comparative analyses of otic microbiomes revealed that mite-infected Santa Catalina and San Clemente Island foxes exhibited reduced bacterial diversity, skewed abundance towards the opportunistic pathogen Staphylococcus pseudintermedius and disrupted microbial community networks. However, Santa Catalina Island foxes uniquely harboured Fusobacterium and Prevotella bacteria as potential keystone taxa. These bacteria have previously been associated with colorectal cancer and may predispose Santa Catalina Island foxes to an elevated cancer risk. In contrast, mite-infected San Nicolas Island foxes maintained high bacterial diversity and robust microbial community networks, suggesting that they harbour more resilient microbiomes. Considered together, our results highlight the diverse eco-evolutionary factors influencing commensal microbial communities and their hosts and underscore how the microbiome can contribute to disease outcomes.

Insights into the gut microbiome of vitiligo patients from India

BACKGROUND

Vitiligo is an autoimmune disease characterized by loss of pigmentation in the skin. It affects 0.4 to 2% of the global population, but the factors that trigger autoimmunity remain elusive. Previous work on several immune-mediated dermatological disorders has illuminated the substantial roles of the gut microbiome in disease pathogenesis. Here, we examined the gut microbiome composition in a cohort of vitiligo patients and healthy controls from India, including patients with a family history of the disease.

RESULTS

Our results show significant alterations in the gut microbiome of vitiligo patients compared to healthy controls, affecting taxonomic and functional profiles as well as community structure. We observed a reduction in the abundance of several bacterial taxa commonly associated with a healthy gut microbiome and noted a decrease in the abundance of SCFA (Short Chain Fatty Acids) producing taxa in the vitiligo group. Observation of a higher abundance of genes linked to bacteria-mediated degradation of intestinal mucus suggested a potential compromise of the gut mucus barrier in vitiligo. Functional analysis also revealed a higher abundance of fatty acid and lipid metabolism-related genes in the vitiligo group. Combined analysis with data from a French cohort of vitiligo also led to the identification of common genera differentiating healthy and gut microbiome across populations.

CONCLUSION

Our observations, together with available data, strengthen the role of gut microbiome dysbiosis in symptom exacerbation and possibly pathogenesis in vitiligo. The reported microbiome changes also showed similarities with other autoimmune disorders, suggesting common gut microbiome-mediated mechanisms in autoimmune diseases. Further investigation can lead to the exploration of dietary interventions and probiotics for the management of these conditions.

Endophytic microbial diversity associated with commercial cultivar and crop wild relative banana variety could provide clues for microbial community management

Endophytes, microorganisms inhabiting internal plant tissues, play a pivotal role in plant growth and disease resistance. Moreover, previous studies have established that Musa plants derive disease protective functions from their microbiome. Notably, one of the crop wild relatives of banana, the Calcutta 4 variety, exhibits resistance to various phytopathogens such as Pseudocercospora fijiensis (P. fijiensis), while the Williams commercial cultivar (cv.) is highly susceptible. Therefore, this study aims primarily to characterize and compare the endophytic microbiota composition of Calcutta 4 and Williams banana plants when grown sympatrically. Alongside, differences in endophytic microbiome between plant sections (shoot or roots), growth phases (in vitro or greenhouse) and fitness factors such as the addition of plant growth-promoting bacteria Bacillus subtilis EA-CB0575 (T2 treatment) or infection by P. fijiensis (T3 treatment) were examined. Both culture-dependent and -independent techniques were used to evaluate these differences and assess the culturability of banana endophytes under varying conditions. Microbial cultures resulted in 331 isolates distributed across 54 genera when all treatments were evaluated, whereas 16 S sequencing produced 9510 ASVs assigned in 1456 genera. Alpha and beta diversity exhibited significant differences based on plant section, with an increase in phylogenetic diversity observed in plants with pathogen infection (T3) compared to control plants (T1). Additionally, four differentially abundant genera associated with nitrogen metabolism were identified in T3 plants and seven genera showed differential abundance when comparing varieties. When culture-dependent and -independent methods were compared, it was found that isolates represented 3.7 % of the genera detected by culture-independent methods, accounting for 12-41 % of the total data depending on the treatment. These results are crucial for proposing management strategies derived from crop wild relatives to enhance the resilience of susceptible commercial varieties against fitness factors affecting crop development. Additionally, they help to decipher the pathogenic effects of P. fijiensis in banana plants and advance the understanding of how plant domestication influences the endosphere.

Oral-to-rectum microbial transmission in orthopedic patients without a history of intestinal disorders

The enrichment of oral taxa in the gut has recently been reported as a notable alteration in the microbial balance in patients with intestinal disorders. However, translocation in populations without such diseases remains controversial. In this study, we examined 49 pairs of tongue and rectal samples collected from orthopedic patients without a history of intestinal disorders to verify the presence of oral taxa in the rectal microbiota. The bacterial composition of each sample was determined using 16S rRNA gene sequencing and amplicon sequence variant (ASV) analysis. Although the bacterial compositions of the tongue and rectal microbiota were distinctly different, tongue ASVs were detected in 67.3% of the participants and accounted for 0.0%-9.37% of the rectal microbiota. Particularly, Streptococcus salivarius, Fusobacterium nucleatum, and Streptococcus parasanguinis were abundant in the rectal microbiota. According to the network analysis, tongue taxa, such as S. salivarius and S. parasanguinis, formed a cohabiting group with Klebsiella pneumoniae and Alistipes finegoldii in the rectal microbiota. The total abundance of tongue ASVs in the rectal microbiota was significantly higher in participants with older age, hypertension, and proton pump inhibitor (PPI) use. Our study presents an extensive translocation of oral taxa to the rectum of a population without intestinal disorders and suggests that aging, hypertension, and PPI use are associated with an increased abundance of oral taxa and potential pathogenic bacteria in the rectal microbiota.

Correlation between bacterial microbiome and Legionella species in water from public bath facilities by 16S rRNA gene amplicon sequencing

Public bath facilities are a major source of Legionella infections in Japan. In this study, we performed 16S rRNA gene amplicon sequencing to characterize the bacterial community in bath and shower water from public bath facilities, along with chemical parameters, and investigated the effect of the bacterial microbiome on the presence of Legionella species. Although no significant difference in bacterial community richness was observed between bath and shower water samples, there was a remarkable difference in the bacterial community structure between them. Distance-based redundancy analysis revealed that several factors (free residual chlorine, pH, and conductivity) were correlated with the bacterial community in bath water. The most abundant bacterial genera in the samples were Pseudomonas (13.7%) in bath water and Phreatobacter (13.6%) in shower water, as indicated by the taxonomic composition, and the dominant bacteria differed between these environmental samples. Legionella pneumophila was the most frequently detected Legionella species, with additional 15 other Legionella species detected in water samples. In Legionella-positive water samples, several unassigned and uncultured bacteria were enriched together. In addition, the co-occurrence network showed that Legionella was strongly interconnected with two uncultured bacteria. Corynebacterium and Sphingomonas negatively correlated with Legionella species. The present study reveals the ecology of Legionella species, especially their interactions with other bacteria that are poorly understood to date.

IMPORTANCE

Public bath facilities are major sources of sporadic cases and outbreaks of Legionella infections. Recently, 16S rRNA gene amplicon sequencing has been used to analyze bacterial characteristics in various water samples from both artificial and natural environments, with a particular focus on Legionella bacterial species. However, the relationship between the bacterial community and Legionella species in the water from public bath facilities remains unclear. In terms of hygiene management, it is important to reduce the growth of Legionella species by disinfecting the water in public bath facilities. Our findings contribute to the establishment of appropriate hygiene management practices and provide a basis for understanding the potential health effects of using bath and shower water available in public bath facilities.

Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe

BACKGROUND

The widespread availability of antiretroviral therapy (ART) has dramatically reduced mortality and improved life expectancy for people living with HIV (PLWH). However, even with HIV-1 suppression, chronic immune activation and elevated inflammation persist and have been linked to a pro-inflammatory gut microbiome composition and compromised intestinal barrier integrity. PLWH in urban versus rural areas of sub-Saharan Africa experience differences in environmental factors that may impact the gut microbiome and immune system, in response to ART, yet this has not previously been investigated in these groups. To address this, we measured T cell activation/exhaustion/trafficking markers, plasma inflammatory markers, and fecal microbiome composition in PLWH and healthy participants recruited from an urban clinic in the city of Harare, Zimbabwe, and a district hospital that services surrounding rural villages. PLWH were either ART naïve at baseline and sampled again after 24 weeks of first-line ART and the antibiotic cotrimoxazole or were ART-experienced at both timepoints.

RESULTS

Although expected reductions in the inflammatory marker IL-6, T-cell activation, and exhaustion were observed with ART-induced viral suppression, these changes were much more pronounced in the urban versus the rural area. Gut microbiome composition was the most highly altered from healthy controls in ART experienced PLWH, and characterized by both reduced alpha diversity and altered composition. However, gut microbiome composition showed a pronounced relationship with T cell activation and exhaustion in ART-naïve PLWH, suggesting a particularly significant role for the gut microbiome in disease progression in uncontrolled infection. Elevated immune exhaustion after 24 weeks of ART did correlate with both living in the rural location and a more Prevotella-rich/Bacteroides-poor microbiome type, suggesting a potential role for rural-associated microbiome differences or their co-variates in the muted improvements in immune exhaustion in the rural area.

CONCLUSION

Successful ART was less effective at reducing gut microbiome-associated inflammation and T cell activation in PLWH in rural versus urban Zimbabwe, suggesting that individuals on ART in rural areas of Zimbabwe may be more vulnerable to co-morbidity related to sustained immune dysfunction in treated infection. Video Abstract.

Combining compositional data sets introduces error in covariance network reconstruction

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

Disturbance frequency directs microbial community succession in marine biofilms exposed to shear

IMPORTANCE

Disturbances are major drivers of community succession in many microbial systems; however, relatively little is known about marine biofilm community succession, especially under antifouling disturbance. Antifouling technologies exert strong local disturbances on marine biofilms, and resulting biomass losses can be accompanied by shifts in biofilm community composition and succession. We address this gap in knowledge by bridging microbial ecology with antifouling technology development. We show that disturbance by shear can strongly alter marine biofilm community succession, acting as a selective filter influenced by frequency of exposure. Examining marine biofilm succession patterns with and without shear revealed stable associations between key prokaryotic and eukaryotic taxa, highlighting the importance of cross-domain assessment in future marine biofilm research. Describing how compounded top-down and bottom-up disturbances shape the succession of marine biofilms is valuable for understanding the assembly and stability of these complex microbial communities and predicting species invasiveness.

Antiretroviral treatment is less effective at reducing gut microbiome-associated inflammation and T cell activation in people living with HIV in rural versus urban Zimbabwe

The widespread availability of antiretroviral therapy (ART) for people living with HIV (PLWH) has dramatically reduced mortality and improved life expectancy. However, even with suppression of HIV-1 replication, chronic immune activation and elevated inflammation persist. Chronic immune activation has been linked to a pro-inflammatory gut microbiome composition, exacerbated by compromised intestinal barrier integrity that occurs after HIV infection. Individuals living in urban versus rural areas of sub-Saharan Africa have differences in environmental factors such as water source or diet that may impact gut microbiome composition, yet immune phenotype and gut microbiome composition response to ART in PLWH living in rural versus urban areas of sub-Saharan Africa have not been compared. Here, we measured immune phenotypes and fecal microbiome composition in PLWH and healthy participants recruited from the urban Mabvuku polyclinic in the city of Harare, Zimbabwe and the Mutoko District hospital located in a district 146 km from Harare that services surrounding rural villages. PLWH were either ART naïve at baseline and sampled again after 24 weeks of treatment with efavirenz/lamivudine/tenofovir disoproxil fumarate (EFV/3TC/TDF) and the prophylactic antibiotic cotrimoxazole or were ART experienced at both timepoints. Although expected reductions in the inflammatory marker IL-6, T-cell activation, and exhaustion were observed in individuals who had suppressed HIV-1 with treatment, these changes were significant only when considering individuals in the urban and not the rural area. Gut microbiome composition showed more marked differences from healthy controls in the ART experienced compared to ART naïve cohort, and consistent longitudinal changes were also observed in ART naïve PLWH after 24 weeks of treatment, including a reduction in alpha diversity and altered composition. However, gut microbiome composition showed a more pronounced relationship with chronic immune activation and exhaustion phenotypes in the ART naïve compared to ART experienced PLWH, suggesting a particularly significant role for the gut microbiome in disease progression in uncontrolled infection.

Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults

BACKGROUND

The clinical outcomes of SARS-CoV-2 infection vary in severity, potentially influenced by the resident human microbiota. There is limited consensus on conserved microbiome changes in response to SARS-CoV-2 infection, with many studies focusing on severely ill individuals. This study aimed to assess the variation in the upper respiratory tract microbiome using saliva specimens in a cohort of individuals with primarily mild to moderate disease.

METHODS

In early 2020, a cohort of 831 adults without known SARS-CoV-2 infection was followed over a six-month period to assess the occurrence and natural history of SARS-CoV-2 infection. From this cohort, 81 participants with a SARS-CoV-2 infection, along with 57 unexposed counterparts were selected with a total of 748 serial saliva samples were collected for analysis. Total bacterial abundance, composition, population structure, and gene function of the salivary microbiome were measured using 16S rRNA gene and shotgun metagenomic sequencing.

FINDINGS

The salivary microbiome remained stable in unexposed individuals over the six-month study period, as evidenced by all measured metrics. Similarly, participants with mild to moderate SARS-CoV-2 infection showed microbiome stability throughout and after their infection. However, there were significant reductions in microbiome diversity among SARS-CoV-2-positive participants with severe symptoms early after infection. Over time, the microbiome diversity in these participants showed signs of recovery.

INTERPRETATION

These findings demonstrate the resilience of the salivary microbiome in relation to SARS-CoV-2 infection. Mild to moderate infections did not significantly disrupt the stability of the salivary microbiome, suggesting its ability to maintain its composition and function. However, severe SARS-CoV-2 infection was associated with temporary reductions in microbiome diversity, indicating the limits of microbiome resilience in the face of severe infection.

FUNDING

This project was supported in part by Danone North America and grants from the National Institutes of Health, United States.

Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine

Preterm infants with very low birthweight are at serious risk for necrotizing enterocolitis. To functionally analyse the principles of three successful preventive NEC regimens, we characterize fecal samples of 55 infants (<1500 g, n = 383, female = 22) longitudinally (two weeks) with respect to gut microbiome profiles (bacteria, archaea, fungi, viruses; targeted 16S rRNA gene sequencing and shotgun metagenomics), microbial function, virulence factors, antibiotic resistances and metabolic profiles, including human milk oligosaccharides (HMOs) and short-chain fatty acids (German Registry of Clinical Trials, No.: DRKS00009290). Regimens including probiotic Bifidobacterium longum subsp. infantis NCDO 2203 supplementation affect microbiome development globally, pointing toward the genomic potential to convert HMOs. Engraftment of NCDO 2203 is associated with a substantial reduction of microbiome-associated antibiotic resistance as compared to regimens using probiotic Lactobacillus rhamnosus LCR 35 or no supplementation. Crucially, the beneficial effects of Bifidobacterium longum subsp. infantis NCDO 2203 supplementation depends on simultaneous feeding with HMOs. We demonstrate that preventive regimens have the highest impact on development and maturation of the gastrointestinal microbiome, enabling the establishment of a resilient microbial ecosystem that reduces pathogenic threats in at-risk preterm infants.

Fecal Microbiota, Forage Nutrients, and Metabolic Responses of Horses Grazing Warm- and Cool-Season Grass Pastures

Integrating warm-season grasses into cool-season equine grazing systems can increase pasture availability during summer months. The objective of this study was to evaluate effects of this management strategy on the fecal microbiome and relationships between fecal microbiota, forage nutrients, and metabolic responses of grazing horses. Fecal samples were collected from 8 mares after grazing cool-season pasture in spring, warm-season pasture in summer, and cool-season pasture in fall as well as after adaptation to standardized hay diets prior to spring grazing and at the end of the grazing season. Random forest classification was able to predict forage type based on microbial composition (accuracy: 0.90 ± 0.09); regression predicted forage crude protein (CP) and non-structural carbohydrate (NSC) concentrations (p < 0.0001). Akkermansia and Clostridium butyricum were enriched in horses grazing warm-season pasture and were positively correlated with CP and negatively with NSC; Clostridum butyricum was negatively correlated with peak plasma glucose concentrations following oral sugar tests (p ≤ 0.05). These results indicate that distinct shifts in the equine fecal microbiota occur in response different forages. Based on relationships identified between the microbiota, forage nutrients, and metabolic responses, further research should focus on the roles of Akkermansia spp. and Clostridium butyricum within the equine hindgut.

Altered Faecal Microbiota Composition and Structure of Ghanaian Children with Acute Gastroenteritis

Acute gastroenteritis (AGE) is a disease of global public health importance. Recent studies show that children with AGE have an altered gut microbiota relative to non-AGE controls. Yet, how the gut microbiota differs in Ghanaian children with and without AGE remains unclear. Here, we explore the 16S rRNA gene-based faecal microbiota profiles of Ghanaian children five years of age and younger, comprising 57 AGE cases and 50 healthy controls. We found that AGE cases were associated with lower microbial diversity and altered microbial sequence profiles relative to the controls. The faecal microbiota of AGE cases was enriched for disease-associated bacterial genera, including Enterococcus, Streptococcus, and Staphylococcus. In contrast, the faecal microbiota of controls was enriched for potentially beneficial genera, including Faecalibacterium, Prevotella, Ruminococcus, and Bacteroides. Lastly, distinct microbial correlation network characteristics were observed between AGE cases and controls, thereby supporting broad differences in faecal microbiota structure. Altogether, we show that the faecal microbiota of Ghanaian children with AGE differ from controls and are enriched for bacterial genera increasingly associated with diseases.

Longitudinal Study of Fecal Microbiota in Calves with or without Diarrhea Episodes before Weaning

Simple Summary

Animal production is searching for ways to reduce antimicrobial use, and the best way is to avoid their use by maintaining the health of the animals. The microbiota is involved in the host health, and when the fecal microbiota was analyzed in calves that developed or not diarrhea, differences linked to the health status were detected. While changes in the fecal microbiota were observed with time (during the first 2 months of age) in all the calves, the microbiota from the healthy animals presented an earlier stabilization and some changes in low abundant bacteria, which may play a role in the subsequent health status of the animals. Bacteria classified in the families Coriobacteriaceae and Phyllobacteriaceae, and the bacterium Epulopiscium were found in the core of the microbiota of the healthy calves (calves that did not have diarrhea) possibly with a protective probiotic effect. On the other hand, several bacteria, such as Lachnospira, Neisseria and Solibacillus, were found only in the core of the microbiota obtained from calves that had diarrhea, indicating that they could be linked to a higher predisposition to suffer diarrhea. These results can help in the development of new probiotics to promote gut health in calves.

Abstract

The microbiota plays an important role in the development of diarrhea in pre-weaned calves. The characterization of the fecal microbiota in health and disease can be critical to unravel the bacterial dynamics associated with diarrhea and help with its prevention and control. In this study, we aimed to detect changes in the fecal microbiota of calves that experienced early-life diarrhea episodes. Fecal samples were taken from calves remaining healthy and calves with an episode of diarrhea during the study. We sampled at arrival (12 days of age) and after one and two months of life; also, at the time of the diarrhea episode for the diarrheic calves (day 17). Samples were processed to extract total DNA, submitted to 16S rRNA gene sequencing, and bioinformatically analyzed to infer the bacterial populations. Microbiota changes through time were reported for both groups. However, we detected an earlier stabilization in the healthy group. Moreover, we detected changes within low abundant taxa that may play a role in the subsequent health status of the animals. The fecal microbiota of healthy and diarrheic calves showed different dynamics in the diversity through time that may be the reflections of the variations within low-abundant taxa.