Characterization of household microbiomes from three unique cities around the world

This study utilized shotgun metagenomics to characterize household bacterial microbiomes across ten homes in Mysuru, Dubai, and Tucson, revealing significant variations in diversity driven by geographic location and cultural practices, while identifying a global core microbiome dominated by human-associated phyla.

The Gist

Imagine your home isn't just a building made of wood, brick, and glass. Imagine it's a bustling, invisible city. Every surface you touch—the TV remote, the kitchen sink, the toilet rim—is a neighborhood in this city, populated by trillions of tiny, microscopic citizens: bacteria.

This paper is like a global travelogue where scientists acted as "microbial detectives" to map out these invisible cities in three very different neighborhoods of the world: Tucson (USA), Dubai (UAE), and Mysuru (India).

Here is the story of what they found, explained simply.

The Mission: A Global Microbe Census

The researchers wanted to answer a big question: Does the "personality" of the bacteria in our homes change depending on where we live?

They visited 10 homes in each of the three cities. In every home, they swabbed 10 different spots (like the coffee table, the showerhead, and the toilet). They didn't just look at the bacteria; they used high-tech "DNA scanners" (shotgun metagenomics) to read the genetic ID cards of every microbe they found.

The Big Discovery: The "Human Shadow"

The most important finding is that our homes are basically giant mirrors of our own bodies.

No matter if you live in a desert in Arizona, a modern metropolis in the UAE, or a historic city in India, the top three "families" of bacteria in your house are almost always the same. They are:

1. The Skin & Breath Squad: Bacteria that live on our skin and in our mouths.
2. The Gut Crew: Bacteria that live in our stomachs.
3. The Dust Settlers: Bacteria that hang out in the air and settle on surfaces.

The Analogy: Think of your house like a crowded party. Even if the party is in a castle in Dubai or a ranch in Tucson, the guests are mostly the same people: your skin cells, your breath, and your hair. The house just collects whatever you shed.

The Differences: Climate and Culture Change the Vibe

While the "guest list" (the main families) was similar, the specific bacteria and how many of them were there changed based on two main factors: Climate and Culture.

• The Desert Twins (Tucson & Dubai): These two cities have hot, dry, desert climates. Their homes had very similar bacterial communities. It's like two houses in the same neighborhood; the air is dry, the windows are often closed (to keep the AC on), and the bacteria are similar.
• The Outlier (Mysuru, India): This city had a much more diverse and "wild" bacterial population. Why?
  • The Open Window Effect: In Mysuru, people often kept their windows open, letting in more outside air, soil, and rain. In Tucson and Dubai, windows were usually closed.
  • The "Messy" Factor: The researchers found that Mysuru homes had more variety, perhaps due to different cultural habits, cleaning routines, or even the socioeconomic factors that influence how much time people spend cleaning.
  • The Result: Mysuru's bacterial "city" was more chaotic and diverse, while Tucson and Dubai were more uniform and controlled.

The "Danger Zones" vs. The "Quiet Zones"

The scientists looked at specific spots in the house to see which were the most crowded.

• The Party Central (High Diversity): The area under the toilet rim and the kitchen sink were the most diverse.
  • Why? These are "wet zones." Moisture is like a five-star hotel for bacteria. It allows many different types to survive and thrive.
• The Quiet Neighborhoods (Low Diversity): The TV remote and the showerhead had fewer types of bacteria.
  • Why? The TV remote is dry and gets wiped down often. The showerhead gets blasted with water constantly, which washes away the weaker bacteria, leaving only the "tough guys" who can survive the rinse cycle.

The "Core" Microbiome

Despite all the differences, the scientists found a "Core Group" of bacteria that showed up in almost every single house, everywhere.

• The Core Members: Moraxella (a skin bacteria), Acinetobacter, and Pseudomonas.
• The Analogy: Imagine a global chain of coffee shops. No matter if you go to one in New York, London, or Tokyo, you will always find a barista, a coffee machine, and a specific type of chair. These bacteria are the "baristas" of your house—they are always there, regardless of the location.

The "Gross" Factor: Are We Sick?

The study found some bacteria that sound scary, like E. coli and Salmonella (usually found in poop) in the toilet and even on the kitchen sink.

• The Reality Check: Finding their DNA doesn't mean they are alive and ready to make you sick. It just means they were there at some point. It's like finding a receipt from a grocery store in your pocket; it proves you went there, but it doesn't mean you are currently eating the groceries.
• The Takeaway: It highlights the importance of cleaning, especially in the kitchen and bathroom, to keep these "unwanted guests" from multiplying.

The Bottom Line

Your home's microbiome is a unique fingerprint. It is shaped by:

1. Who lives there (you and your family).
2. Where you live (the climate and local environment).
3. What you do (how you clean, whether you open windows, and cultural habits).

The Final Metaphor:
Think of your house as a garden.

• Tucson and Dubai are like two gardens in the same dry climate; they have similar weeds and flowers because the sun and rain are the same.
• Mysuru is like a garden in a different climate with different watering habits; it has a wilder, more chaotic mix of plants because the environment and the gardener's habits are different.

Understanding this helps us realize that we can't just "sterilize" our homes to make them perfect. We need to understand how our habits and our environment shape these invisible communities, so we can keep the good bugs and manage the bad ones.

Technical Summary

1. Problem Statement

The indoor built environment is a complex ecosystem heavily influenced by human activity, cultural practices, climate, and building materials. While previous studies have characterized household microbiomes in specific regions (e.g., the US, UK, China), there is a lack of comparative data across diverse global geographies with varying socio-economic and climatic conditions. Understanding how these factors drive microbial diversity, the existence of a "core" microbiome, and the presence of potential pathogens is critical for assessing public health risks and developing targeted hygiene strategies. This study addresses the gap in global comparative analysis by examining household bacterial communities across three distinct cities: Mysuru (India), Dubai (UAE), and Tucson (USA).

2. Methodology

• Study Design & Sampling:

  • Locations: Ten households were sampled in each of three cities: Mysuru, India (population ~3M); Dubai, UAE (population ~3.8M); and Tucson, Arizona, USA (population ~555k).
  • Sample Sites: Up to 10 specific locations per household were swabbed, including kitchen counters/sinks, coffee tables, TV remotes, showerheads, bathroom sinks, and four distinct toilet areas (seat, rim, bowl, under-rim).
  • Total Samples: 100 samples from Tucson, 100 from Mysuru, and 89 from Dubai (due to missing specific locations in some Dubai homes).
  • Collection: Dual-end swabs dipped in sterile detergent solution (0.15 M NaCl, 0.1% Tween 20) were used to swab surfaces for 15–30 seconds.

• Laboratory Processing:

  • DNA Extraction: Performed using the DNeasy Powersoil Pro Kit with a modification (heating at 65°C for 10 minutes post-lysis).
  • Sequencing: Oxford Nanopore Technology (ONT) MinION Mk1B devices with R10.4.1 flow cells were used.
    • Tucson: Sequenced using the Rapid PCR Barcoding Kit 24 V14.
    • Mysuru: Sequenced on-site using the Rapid Barcoding Kit 96 V14 (PCR-free due to lack of thermocyclers).
    • Dubai: Shipped on dry ice and sequenced in Tucson using the PCR kit.
  • Quality Control: Negative controls were not collected. Samples were sequenced multiple times to ensure sufficient yield.

• Bioinformatics & Analysis:

  • Taxonomic Classification: Reads were processed using Kraken2 (v2.3.1) against a custom database containing all NCBI reference genomes and the non-redundant (nr) database.
  • Filtering: Only bacterial taxa (approx. 70% of reads) were retained; eukaryotic reads (Chordata, Arthropoda) were excluded.
  • Diversity Metrics:
    • Alpha Diversity: Calculated using Shannon, Simpson, Chao, Fisher, and Observed Species indices.
    • Beta Diversity: Bray-Curtis dissimilarity index calculated.
  • Statistical Testing: ANOVA for alpha diversity; PERMANOVA for beta diversity to test significance between cities and household locations.
  • Core Microbiome: Defined as taxa present in ≥90% of samples with a relative abundance ≥1% (higher taxa) or ≥0.1% (species level).

3. Key Results

• Global Diversity Differences:

  • Alpha Diversity: Mysuru households exhibited significantly higher bacterial diversity compared to Dubai and Tucson (ANOVA, p<0.05), regardless of the diversity index used.
  • Beta Diversity: Significant differences were found between cities (PERMANOVA, p<0.001) and between household locations (PERMANOVA, p<0.001). Dubai and Tucson samples clustered more closely together, while Mysuru samples showed greater dispersion.

• Taxonomic Composition:

  • Dominant Phyla: Across all cities, the microbiome was dominated by Pseudomonadota (48–63%), Actinomycetota, and Bacillota.
    • Dubai: Highest Pseudomonadota levels; lowest Actinomycetota.
    • Mysuru: Highest Actinomycetota levels (29%).
    • Tucson: Highest Bacillota levels (7%).
  • Core Microbiome (Global): A core microbiome at the phylum and class levels was identified across all three cities, consisting of Pseudomonadota, Actinomycetota, and Gammaproteobacteria.
  • Core Microbiome (City-Specific):
    • Mysuru: Showed the most diverse core microbiome at the species level, including Escherichia coli, Salmonella enterica, Shigella flexneri, Moraxella osloensis, and Francisella halioticida.
    • Dubai & Tucson: Had smaller core microbiomes at the species level, often lacking the enteric bacteria found in Mysuru.

• Location-Specific Findings:

  • Highest Diversity: The area under the toilet rim consistently showed the highest Shannon diversity across all cities. Kitchen sinks and bathroom sinks also exhibited high diversity.
  • Lowest Diversity: TV remotes and showerheads generally showed lower diversity.
  • Specific Genera:
    • Moraxella was dominant in bathroom/kitchen sinks and toilet areas in Dubai and Tucson.
    • Acinetobacter was highly abundant in kitchen counters in Tucson and bathroom/kitchen sinks in Dubai.
    • Streptococcus was notably more abundant on TV remotes in Tucson.

• Pathogen Detection:

  • Several potential pathogens were detected in the core microbiome, including E. coli, Salmonella enterica, Shigella flexneri, Pseudomonas aeruginosa, and Acinetobacter baumannii. The authors note that DNA detection does not confirm viability but highlights potential health risks.

4. Key Contributions

1. Global Comparative Framework: This is one of the few studies to directly compare household microbiomes across three distinct global cities (India, UAE, USA) using a standardized sampling and sequencing protocol.
2. Identification of Drivers: The study highlights that while the phyla are globally consistent (human-associated), the species composition is driven by local factors.
   • Climate: The similarity between Dubai and Tucson (both arid/desert climates) suggests climate is a major driver, distinct from the semi-arid/steppe climate of Mysuru.
   • Cultural/Human Factors: The higher diversity and presence of enteric bacteria in Mysuru may be linked to open windows (increasing environmental influx), different cleaning habits, or socio-economic factors.
3. Methodological Application: Demonstrates the utility of Oxford Nanopore sequencing for rapid, on-site (Mysuru) and centralized (Tucson/Dubai) metagenomic profiling of built environments.
4. Core Microbiome Definition: Refines the definition of the "core" household microbiome, showing that while high-level taxa are universal, species-level cores are highly location-specific.

5. Significance and Implications

• Public Health: The identification of pathogenic DNA (e.g., Salmonella, Shigella) in household niches underscores the need for targeted hygiene interventions. However, the authors caution that DNA presence does not equate to active infection risk.
• Hygiene Product Development: Understanding that different surfaces harbor distinct microbial communities (e.g., moisture-rich sinks vs. dry remotes) supports the development of "bi-directional hygiene" (or "bygiene") approaches. These strategies aim to reduce pathogens while preserving beneficial or neutral microbes that contribute to a healthy indoor ecosystem.
• Environmental Drivers: The study reinforces that the built microbiome is not static; it is shaped by a complex interplay of climate (humidity/temperature), human behavior (cleaning frequency, window opening), and building materials.
• Future Research: The authors suggest future studies should incorporate longitudinal sampling, detailed metadata on cleaning habits and socio-economic status, and functional metagenomics to understand the metabolic capabilities of these communities.

Limitations Noted:

• Lack of negative controls during sequencing.
• Differences in sequencing kits (PCR vs. PCR-free) between sites.
• Inconsistent sampling of all 10 locations across all 30 homes.
• Cross-sectional design (single time point) prevents analysis of temporal dynamics.
• Seasonal differences in sampling (Winter in US/India vs. Fall in UAE).